This example will use C gigas larvae data.
!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq.gz
!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R2.fastq.gz
!head /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq
@HWI-ST700693:378:C39KLACXX:5:1101:1432:1973 NTTTAGATGGTATTATTATTGATTTTATTTTTTTGG + #41B44242222AAGGIIJJIJJJJJIJJJJJGIIB @HWI-ST700693:378:C39KLACXX:5:1101:1985:1979 NATAGATAAAGGTTATATTGGTGTATATGAGATTAG + #11A42224222>AFGIJJJJIIFHIJJJJIIJJJJ @HWI-ST700693:378:C39KLACXX:5:1101:1887:1990 NATTTATTTGTAAATAGGTAGTTAATTATAATGATT
Running fastQC in IPlant
!ipwd
/iplant/home/sr320/Cgigas_yan_larvae
!iput /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq
!iput /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R2.fastq
!ils
/iplant/home/sr320/Cgigas_yan_larvae: filtered_Y54_Mix_GTGGCC_L005_R1.fastq filtered_Y54_Mix_GTGGCC_L005_R2.fastq
running fastqc in iplant
cd /Volumes/web/cnidarian/
/Volumes/web/cnidarian
!wget http://de.iplantcollaborative.org/dl/d/B2362EE9-1E20-4F72-9724-64F261655EDA/filtered_Y54_Mix_GTGGCC_L005_R1_fastqc.zip
--2014-06-03 14:49:28-- http://de.iplantcollaborative.org/dl/d/B2362EE9-1E20-4F72-9724-64F261655EDA/filtered_Y54_Mix_GTGGCC_L005_R1_fastqc.zip Resolving de.iplantcollaborative.org... 150.135.78.218 Connecting to de.iplantcollaborative.org|150.135.78.218|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [application/zip] Saving to: `filtered_Y54_Mix_GTGGCC_L005_R1_fastqc.zip.1' [ <=> ] 226,475 834K/s in 0.3s 2014-06-03 14:49:30 (834 KB/s) - `filtered_Y54_Mix_GTGGCC_L005_R1_fastqc.zip.1' saved [226475]
!/Volumes/Bay3/Software/FastQC/fastqc /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq -o /Volumes/web/cnidarian/
Started analysis of filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 5% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 10% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 15% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 20% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 25% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 30% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 35% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 40% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 45% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 50% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 55% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 60% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 65% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 70% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 75% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 80% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 85% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 90% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 95% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Approx 100% complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq Analysis complete for filtered_Y54_Mix_GTGGCC_L005_R1.fastq
!/Volumes/Bay3/Software/FastQC/fastqc /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R2.fastq -q -o /Volumes/web/cnidarian/
!echo ">TruSeq Adapter, Index 1\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG\n>Illumina Single End PCR Primer 1\nGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT" \
> YE_overrepresent.txt
!cat YE_overrepresent.txt
>TruSeq Adapter, Index 1 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG >Illumina Single End PCR Primer 1 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT
!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \
-o /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R1_tr.fastq \
-o /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R2_tr.fastq \
/Volumes/web/cnidarian/YE_overrepresent.txt \
/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq \
/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R2.fastq
Scale used: 2.2 Phred: 33 Within-read Skew: Position 4 from the start of reads is skewed! Within-read Skew: Position 5 from the start of reads is skewed! Within-read Skew: Position 6 from the start of reads is skewed! Within-read Skew: Position 7 from the start of reads is skewed! Within-read Skew: Position 8 from the start of reads is skewed! Within-read Skew: Position 9 from the start of reads is skewed! Within-read Skew: Position 10 from the start of reads is skewed! Within-read Skew: Position 12 from the start of reads is skewed! Within-read Skew: Position 14 from the start of reads is skewed! Within-read Skew: Position 16 from the start of reads is skewed! Within-read Skew: Position 17 from the start of reads is skewed! Within-read Skew: Position 4 from the end of reads is skewed! Within-read Skew: Position 6 from the end of reads is skewed! Within-read Skew: Position 7 from the end of reads is skewed! Within-read Skew: Position 8 from the end of reads is skewed! Within-read Skew: Position 11 from the end of reads is skewed! Within-read Skew: Position 13 from the end of reads is skewed! Within-read Skew: Position 14 from the end of reads is skewed! Within-read Skew: Position 15 from the end of reads is skewed! Within-read Skew: Position 16 from the end of reads is skewed! Within-read Skew: Position 6 from the end of reads is skewed! Within-read Skew: Position 7 from the end of reads is skewed! Within-read Skew: Position 8 from the end of reads is skewed! Within-read Skew: Position 9 from the end of reads is skewed! Within-read Skew: Position 10 from the end of reads is skewed! Within-read Skew: Position 11 from the end of reads is skewed! Within-read Skew: Position 12 from the end of reads is skewed! Within-read Skew: Position 13 from the end of reads is skewed! Within-read Skew: Position 14 from the end of reads is skewed! Within-read Skew: Position 15 from the end of reads is skewed! Within-read Skew: Position 16 from the end of reads is skewed! Within-read Skew: Position 17 from the end of reads is skewed! Warning: Too much skewing found (23), disabling skew clipping Threshold used: 751 out of 300000 Adapter TruSeq Adapter, Index 1 (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG): counted 29857 at the 'start' of '/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq', clip set to 2 Files: 2 Total reads: 15646291 Too short after clip: 2233969 Clipped 'start' reads (/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq): Count 949702, Mean: 2.32, Sd: 0.51 Trimmed 276107 reads (/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R1.fastq) by an average of 7.78 bases on quality < 7 Trimmed 540082 reads (/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y54_Mix_GTGGCC_L005_R2.fastq) by an average of 22.66 bases on quality < 7
!/Volumes/Bay3/Software/FastQC/fastqc /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R1_tr.fastq -q -o /Volumes/web/cnidarian/
!/Volumes/Bay3/Software/FastQC/fastqc /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R2_tr.fastq -q -o /Volumes/web/cnidarian/
! /Volumes/Bay3/Software/BSMAP/bsmap-2.74/bsmap \
-a /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R1_tr.fastq \
-b /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R2_tr.fastq \
-d /Volumes/web/cnidarian/oyster.v9.fa \
-o /Volumes/web/cnidarian/BiLar_YE_mix_t.sam \
-p 4
BSMAP v2.74 Start at: Tue Jun 3 15:33:16 2014 Input reference file: /Volumes/web/cnidarian/oyster.v9.fa (format: FASTA) Load in 11969 db seqs, total size 558601156 bp. 30 secs passed total_kmers: 43046721 Create seed table. 119 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(4 threads) Input read file #1: /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R1_tr.fastq (format: FASTQ) Input read file #2: /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R2_tr.fastq (format: FASTQ) Output file: /Volumes/web/cnidarian/BiLar_YE_mix_t.sam (format: SAM) Thread #1: 50000 read pairs finished. 290 secs passed Thread #0: 150000 read pairs finished. 294 secs passed Thread #2: 100000 read pairs finished. 294 secs passed Thread #3: 200000 read pairs finished. 297 secs passed Thread #1: 250000 read pairs finished. 446 secs passed Thread #0: 300000 read pairs finished. 447 secs passed Thread #2: 350000 read pairs finished. 449 secs passed Thread #3: 400000 read pairs finished. 450 secs passed Thread #1: 450000 read pairs finished. 589 secs passed Thread #0: 500000 read pairs finished. 591 secs passed Thread #2: 550000 read pairs finished. 593 secs passed Thread #3: 600000 read pairs finished. 597 secs passed Thread #1: 650000 read pairs finished. 724 secs passed Thread #0: 700000 read pairs finished. 724 secs passed Thread #2: 750000 read pairs finished. 728 secs passed Thread #3: 800000 read pairs finished. 732 secs passed Thread #0: 900000 read pairs finished. 848 secs passed Thread #1: 850000 read pairs finished. 848 secs passed Thread #2: 950000 read pairs finished. 850 secs passed Thread #3: 1000000 read pairs finished. 856 secs passed Thread #0: 1050000 read pairs finished. 979 secs passed Thread #1: 1100000 read pairs finished. 981 secs passed Thread #2: 1150000 read pairs finished. 982 secs passed Thread #3: 1200000 read pairs finished. 989 secs passed Thread #0: 1250000 read pairs finished. 1104 secs passed Thread #1: 1300000 read pairs finished. 1105 secs passed Thread #2: 1350000 read pairs finished. 1107 secs passed Thread #3: 1400000 read pairs finished. 1114 secs passed Thread #0: 1450000 read pairs finished. 1227 secs passed Thread #1: 1500000 read pairs finished. 1230 secs passed Thread #2: 1550000 read pairs finished. 1231 secs passed Thread #3: 1600000 read pairs finished. 1239 secs passed Thread #0: 1650000 read pairs finished. 1377 secs passed Thread #1: 1700000 read pairs finished. 1382 secs passed Thread #2: 1750000 read pairs finished. 1411 secs passed Thread #3: 1800000 read pairs finished. 1411 secs passed Thread #0: 1850000 read pairs finished. 1460 secs passed Thread #1: 1900000 read pairs finished. 1602 secs passed Thread #2: 1950000 read pairs finished. 1604 secs passed Thread #3: 2000000 read pairs finished. 1608 secs passed Thread #0: 2050000 read pairs finished. 1651 secs passed Thread #1: 2100000 read pairs finished. 1797 secs passed Thread #2: 2150000 read pairs finished. 1798 secs passed Thread #3: 2200000 read pairs finished. 1802 secs passed Thread #0: 2250000 read pairs finished. 1848 secs passed Thread #1: 2300000 read pairs finished. 1992 secs passed Thread #2: 2350000 read pairs finished. 1993 secs passed Thread #3: 2400000 read pairs finished. 1996 secs passed Thread #0: 2450000 read pairs finished. 2040 secs passed Thread #1: 2500000 read pairs finished. 2143 secs passed Thread #2: 2550000 read pairs finished. 2144 secs passed Thread #3: 2600000 read pairs finished. 2145 secs passed Thread #0: 2650000 read pairs finished. 2173 secs passed Thread #1: 2700000 read pairs finished. 2268 secs passed Thread #2: 2750000 read pairs finished. 2270 secs passed Thread #3: 2800000 read pairs finished. 2272 secs passed Thread #0: 2850000 read pairs finished. 2300 secs passed Thread #1: 2900000 read pairs finished. 2396 secs passed Thread #2: 2950000 read pairs finished. 2400 secs passed Thread #3: 3000000 read pairs finished. 2402 secs passed Thread #0: 3050000 read pairs finished. 2430 secs passed Thread #1: 3100000 read pairs finished. 2526 secs passed Thread #2: 3150000 read pairs finished. 2529 secs passed Thread #3: 3200000 read pairs finished. 2532 secs passed Thread #0: 3250000 read pairs finished. 2558 secs passed Thread #1: 3300000 read pairs finished. 2651 secs passed Thread #2: 3350000 read pairs finished. 2655 secs passed Thread #3: 3400000 read pairs finished. 2658 secs passed Thread #0: 3450000 read pairs finished. 2683 secs passed Thread #1: 3500000 read pairs finished. 2784 secs passed Thread #2: 3550000 read pairs finished. 2788 secs passed Thread #3: 3600000 read pairs finished. 2793 secs passed Thread #0: 3650000 read pairs finished. 2822 secs passed Thread #1: 3700000 read pairs finished. 2932 secs passed Thread #2: 3750000 read pairs finished. 2938 secs passed Thread #3: 3800000 read pairs finished. 2945 secs passed Thread #0: 3850000 read pairs finished. 2969 secs passed Thread #1: 3900000 read pairs finished. 3070 secs passed Thread #2: 3950000 read pairs finished. 3073 secs passed Thread #3: 4000000 read pairs finished. 3082 secs passed Thread #0: 4050000 read pairs finished. 3105 secs passed Thread #1: 4100000 read pairs finished. 3204 secs passed Thread #2: 4150000 read pairs finished. 3207 secs passed Thread #3: 4200000 read pairs finished. 3215 secs passed Thread #0: 4250000 read pairs finished. 3236 secs passed Thread #1: 4300000 read pairs finished. 3333 secs passed Thread #2: 4350000 read pairs finished. 3336 secs passed Thread #3: 4400000 read pairs finished. 3344 secs passed Thread #0: 4450000 read pairs finished. 3364 secs passed Thread #1: 4500000 read pairs finished. 3462 secs passed Thread #2: 4550000 read pairs finished. 3464 secs passed Thread #3: 4600000 read pairs finished. 3474 secs passed Thread #0: 4650000 read pairs finished. 3494 secs passed Thread #1: 4700000 read pairs finished. 3600 secs passed Thread #2: 4750000 read pairs finished. 3603 secs passed Thread #3: 4800000 read pairs finished. 3615 secs passed Thread #0: 4850000 read pairs finished. 3637 secs passed Thread #1: 4900000 read pairs finished. 3734 secs passed Thread #2: 4950000 read pairs finished. 3736 secs passed Thread #3: 5000000 read pairs finished. 3748 secs passed Thread #0: 5050000 read pairs finished. 3766 secs passed Thread #1: 5100000 read pairs finished. 3864 secs passed Thread #2: 5150000 read pairs finished. 3866 secs passed Thread #3: 5200000 read pairs finished. 3880 secs passed Thread #0: 5250000 read pairs finished. 3897 secs passed Thread #1: 5300000 read pairs finished. 3995 secs passed Thread #2: 5350000 read pairs finished. 3996 secs passed Thread #3: 5400000 read pairs finished. 4010 secs passed Thread #0: 5450000 read pairs finished. 4029 secs passed Thread #1: 5500000 read pairs finished. 4132 secs passed Thread #2: 5550000 read pairs finished. 4132 secs passed Thread #3: 5600000 read pairs finished. 4148 secs passed Thread #0: 5650000 read pairs finished. 4164 secs passed Thread #1: 5700000 read pairs finished. 4261 secs passed Thread #2: 5750000 read pairs finished. 4262 secs passed Thread #3: 5800000 read pairs finished. 4277 secs passed Thread #0: 5850000 read pairs finished. 4293 secs passed Thread #1: 5900000 read pairs finished. 4389 secs passed Thread #2: 5950000 read pairs finished. 4390 secs passed Thread #3: 6000000 read pairs finished. 4405 secs passed Thread #0: 6050000 read pairs finished. 4421 secs passed Thread #1: 6100000 read pairs finished. 4517 secs passed Thread #2: 6150000 read pairs finished. 4519 secs passed Thread #3: 6200000 read pairs finished. 4534 secs passed Thread #0: 6250000 read pairs finished. 4549 secs passed Thread #1: 6300000 read pairs finished. 4647 secs passed Thread #2: 6350000 read pairs finished. 4650 secs passed Thread #3: 6400000 read pairs finished. 4668 secs passed Thread #0: 6450000 read pairs finished. 4681 secs passed Thread #1: 6500000 read pairs finished. 4774 secs passed Thread #2: 6550000 read pairs finished. 4778 secs passed Thread #3: 6600000 read pairs finished. 4797 secs passed Thread #0: 6650000 read pairs finished. 4815 secs passed Thread #1: 6700000 read pairs finished. 4909 secs passed Thread #2: 6750000 read pairs finished. 4913 secs passed Thread #3: 6800000 read pairs finished. 4930 secs passed Thread #0: 6850000 read pairs finished. 4942 secs passed Thread #1: 6900000 read pairs finished. 5035 secs passed Thread #2: 6950000 read pairs finished. 5038 secs passed Thread #3: 7000000 read pairs finished. 5057 secs passed Thread #0: 7050000 read pairs finished. 5071 secs passed Thread #1: 7100000 read pairs finished. 5168 secs passed Thread #2: 7150000 read pairs finished. 5172 secs passed Thread #3: 7200000 read pairs finished. 5191 secs passed Thread #0: 7250000 read pairs finished. 5202 secs passed Thread #1: 7300000 read pairs finished. 5296 secs passed Thread #2: 7350000 read pairs finished. 5300 secs passed Thread #3: 7400000 read pairs finished. 5319 secs passed Thread #0: 7450000 read pairs finished. 5331 secs passed Thread #1: 7500000 read pairs finished. 5424 secs passed Thread #2: 7550000 read pairs finished. 5428 secs passed Thread #3: 7600000 read pairs finished. 5447 secs passed Thread #0: 7650000 read pairs finished. 5457 secs passed Thread #1: 7700000 read pairs finished. 5550 secs passed Thread #2: 7750000 read pairs finished. 5556 secs passed Thread #3: 7800000 read pairs finished. 5575 secs passed Thread #0: 7850000 read pairs finished. 5584 secs passed Thread #1: 7900000 read pairs finished. 5676 secs passed Thread #2: 7950000 read pairs finished. 5682 secs passed Thread #3: 8000000 read pairs finished. 5699 secs passed Thread #0: 8050000 read pairs finished. 5710 secs passed Thread #1: 8100000 read pairs finished. 5802 secs passed Thread #2: 8150000 read pairs finished. 5808 secs passed Thread #3: 8200000 read pairs finished. 5827 secs passed Thread #0: 8250000 read pairs finished. 5837 secs passed Thread #1: 8300000 read pairs finished. 5928 secs passed Thread #2: 8350000 read pairs finished. 5935 secs passed Thread #3: 8400000 read pairs finished. 5954 secs passed Thread #0: 8450000 read pairs finished. 5963 secs passed Thread #1: 8500000 read pairs finished. 6054 secs passed Thread #2: 8550000 read pairs finished. 6061 secs passed Thread #3: 8600000 read pairs finished. 6080 secs passed Thread #0: 8650000 read pairs finished. 6089 secs passed Thread #1: 8700000 read pairs finished. 6185 secs passed Thread #2: 8750000 read pairs finished. 6192 secs passed Thread #3: 8800000 read pairs finished. 6213 secs passed Thread #0: 8850000 read pairs finished. 6222 secs passed Thread #1: 8900000 read pairs finished. 6316 secs passed Thread #2: 8950000 read pairs finished. 6323 secs passed Thread #3: 9000000 read pairs finished. 6342 secs passed Thread #0: 9050000 read pairs finished. 6350 secs passed Thread #1: 9100000 read pairs finished. 6454 secs passed Thread #2: 9150000 read pairs finished. 6461 secs passed Thread #3: 9200000 read pairs finished. 6485 secs passed Thread #0: 9250000 read pairs finished. 6493 secs passed Thread #1: 9300000 read pairs finished. 6605 secs passed Thread #2: 9350000 read pairs finished. 6611 secs passed Thread #3: 9400000 read pairs finished. 6633 secs passed Thread #0: 9450000 read pairs finished. 6639 secs passed Thread #1: 9500000 read pairs finished. 6735 secs passed Thread #2: 9550000 read pairs finished. 6741 secs passed Thread #3: 9600000 read pairs finished. 6762 secs passed Thread #0: 9650000 read pairs finished. 6768 secs passed Thread #1: 9700000 read pairs finished. 6861 secs passed Thread #2: 9750000 read pairs finished. 6866 secs passed Thread #3: 9800000 read pairs finished. 6889 secs passed Thread #0: 9850000 read pairs finished. 6895 secs passed Thread #1: 9900000 read pairs finished. 6990 secs passed Thread #2: 9950000 read pairs finished. 6995 secs passed Thread #3: 10000000 read pairs finished. 7018 secs passed Thread #0: 10050000 read pairs finished. 7023 secs passed Thread #1: 10100000 read pairs finished. 7116 secs passed Thread #2: 10150000 read pairs finished. 7122 secs passed Thread #3: 10200000 read pairs finished. 7147 secs passed Thread #0: 10250000 read pairs finished. 7150 secs passed Thread #1: 10300000 read pairs finished. 7249 secs passed Thread #2: 10350000 read pairs finished. 7257 secs passed Thread #3: 10400000 read pairs finished. 7284 secs passed Thread #0: 10450000 read pairs finished. 7286 secs passed Thread #1: 10500000 read pairs finished. 7378 secs passed Thread #2: 10550000 read pairs finished. 7384 secs passed Thread #0: 10650000 read pairs finished. 7411 secs passed Thread #3: 10600000 read pairs finished. 7423 secs passed Thread #1: 10700000 read pairs finished. 7491 secs passed Thread #2: 10750000 read pairs finished. 7495 secs passed Thread #0: 10800000 read pairs finished. 7549 secs passed Thread #3: 10850000 read pairs finished. 7552 secs passed Thread #1: 10900000 read pairs finished. 7617 secs passed Thread #2: 10950000 read pairs finished. 7622 secs passed Thread #0: 11000000 read pairs finished. 7675 secs passed Thread #3: 11050000 read pairs finished. 7678 secs passed Thread #1: 11100000 read pairs finished. 7741 secs passed Thread #2: 11150000 read pairs finished. 7746 secs passed Thread #0: 11200000 read pairs finished. 7799 secs passed Thread #3: 11250000 read pairs finished. 7804 secs passed Thread #1: 11300000 read pairs finished. 7865 secs passed Thread #2: 11350000 read pairs finished. 7870 secs passed Thread #0: 11400000 read pairs finished. 7923 secs passed Thread #3: 11450000 read pairs finished. 7929 secs passed Thread #1: 11500000 read pairs finished. 7989 secs passed Thread #2: 11550000 read pairs finished. 7996 secs passed Thread #0: 11600000 read pairs finished. 8047 secs passed Thread #3: 11650000 read pairs finished. 8054 secs passed Thread #1: 11700000 read pairs finished. 8114 secs passed Thread #2: 11750000 read pairs finished. 8121 secs passed Thread #0: 11800000 read pairs finished. 8173 secs passed Thread #3: 11850000 read pairs finished. 8182 secs passed Thread #1: 11900000 read pairs finished. 8243 secs passed Thread #2: 11950000 read pairs finished. 8249 secs passed Thread #0: 12000000 read pairs finished. 8300 secs passed Thread #3: 12050000 read pairs finished. 8311 secs passed Thread #1: 12100000 read pairs finished. 8370 secs passed Thread #2: 12150000 read pairs finished. 8375 secs passed Thread #0: 12200000 read pairs finished. 8425 secs passed Thread #3: 12250000 read pairs finished. 8437 secs passed Thread #1: 12300000 read pairs finished. 8495 secs passed Thread #2: 12350000 read pairs finished. 8500 secs passed Thread #0: 12400000 read pairs finished. 8550 secs passed Thread #3: 12450000 read pairs finished. 8563 secs passed Thread #1: 12500000 read pairs finished. 8619 secs passed Thread #2: 12550000 read pairs finished. 8625 secs passed Thread #0: 12600000 read pairs finished. 8674 secs passed Thread #3: 12650000 read pairs finished. 8688 secs passed Thread #1: 12700000 read pairs finished. 8744 secs passed Thread #2: 12750000 read pairs finished. 8750 secs passed Thread #0: 12800000 read pairs finished. 8799 secs passed Thread #3: 12850000 read pairs finished. 8813 secs passed Thread #1: 12900000 read pairs finished. 8868 secs passed Thread #2: 12950000 read pairs finished. 8875 secs passed Thread #0: 13000000 read pairs finished. 8924 secs passed Thread #3: 13050000 read pairs finished. 8938 secs passed Thread #1: 13100000 read pairs finished. 8994 secs passed Thread #2: 13150000 read pairs finished. 9002 secs passed Thread #0: 13200000 read pairs finished. 9050 secs passed Thread #3: 13250000 read pairs finished. 9067 secs passed Thread #3: 13412322 read pairs finished. 9098 secs passed Thread #1: 13300000 read pairs finished. 9115 secs passed Thread #2: 13350000 read pairs finished. 9121 secs passed Thread #0: 13400000 read pairs finished. 9136 secs passed Total number of aligned reads: pairs: 7934451 (59%) single a: 2762270 (21%) single b: 2440630 (18%) Done. Finished at Tue Jun 3 18:05:32 2014 Total time consumed: 9136 secs
! /Users/Shared/Apps/bsmap-2.74/bsmap \
-a /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R1_tr.fastq \
-b /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R2_tr.fastq \
-d /Users/Steven/Downloads/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-o /Volumes/web/cnidarian/BiLar_YE_mix_t_22sm.sam \
-p 8
BSMAP v2.74 Start at: Wed Jun 4 08:22:12 2014 Input reference file: /Users/Steven/Downloads/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 9 secs passed total_kmers: 43046721 Create seed table. 24 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(8 threads) Input read file #1: /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R1_tr.fastq (format: FASTQ) Input read file #2: /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R2_tr.fastq (format: FASTQ) Output file: /Volumes/web/cnidarian/BiLar_YE_mix_t_22sm.sam (format: SAM) Thread #4: 50000 read pairs finished. 70 secs passed Thread #2: 100000 read pairs finished. 73 secs passed Thread #6: 150000 read pairs finished. 73 secs passed Thread #5: 200000 read pairs finished. 74 secs passed Thread #3: 250000 read pairs finished. 76 secs passed Thread #0: 350000 read pairs finished. 76 secs passed Thread #7: 300000 read pairs finished. 77 secs passed Thread #1: 400000 read pairs finished. 78 secs passed Thread #4: 450000 read pairs finished. 119 secs passed Thread #2: 500000 read pairs finished. 122 secs passed Thread #6: 550000 read pairs finished. 123 secs passed Thread #5: 600000 read pairs finished. 124 secs passed Thread #3: 650000 read pairs finished. 125 secs passed Thread #0: 700000 read pairs finished. 126 secs passed Thread #7: 750000 read pairs finished. 128 secs passed Thread #1: 800000 read pairs finished. 129 secs passed Thread #4: 850000 read pairs finished. 169 secs passed Thread #2: 900000 read pairs finished. 173 secs passed Thread #6: 950000 read pairs finished. 174 secs passed Thread #5: 1000000 read pairs finished. 174 secs passed Thread #3: 1050000 read pairs finished. 175 secs passed Thread #0: 1100000 read pairs finished. 176 secs passed Thread #7: 1150000 read pairs finished. 179 secs passed Thread #1: 1200000 read pairs finished. 180 secs passed Thread #4: 1250000 read pairs finished. 219 secs passed Thread #2: 1300000 read pairs finished. 223 secs passed Thread #6: 1350000 read pairs finished. 224 secs passed Thread #5: 1400000 read pairs finished. 347 secs passed Thread #3: 1450000 read pairs finished. 348 secs passed Thread #0: 1500000 read pairs finished. 348 secs passed Thread #7: 1550000 read pairs finished. 348 secs passed Thread #1: 1600000 read pairs finished. 348 secs passed Thread #4: 1650000 read pairs finished. 349 secs passed Thread #2: 1700000 read pairs finished. 349 secs passed Thread #6: 1750000 read pairs finished. 391 secs passed Thread #5: 1800000 read pairs finished. 394 secs passed Thread #3: 1850000 read pairs finished. 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finished. 503 secs passed Thread #1: 2800000 read pairs finished. 504 secs passed Thread #4: 2850000 read pairs finished. 504 secs passed Thread #2: 2900000 read pairs finished. 505 secs passed Thread #6: 2950000 read pairs finished. 547 secs passed Thread #5: 3000000 read pairs finished. 550 secs passed Thread #3: 3050000 read pairs finished. 554 secs passed Thread #0: 3100000 read pairs finished. 554 secs passed Thread #7: 3150000 read pairs finished. 557 secs passed Thread #1: 3200000 read pairs finished. 558 secs passed Thread #4: 3250000 read pairs finished. 559 secs passed Thread #2: 3300000 read pairs finished. 560 secs passed Thread #6: 3350000 read pairs finished. 601 secs passed Thread #5: 3400000 read pairs finished. 603 secs passed Thread #3: 3450000 read pairs finished. 608 secs passed Thread #0: 3500000 read pairs finished. 609 secs passed Thread #7: 3550000 read pairs finished. 612 secs passed Thread #1: 3600000 read pairs finished. 613 secs passed Thread #4: 3650000 read pairs finished. 613 secs passed Thread #2: 3700000 read pairs finished. 614 secs passed Thread #6: 3750000 read pairs finished. 655 secs passed Thread #5: 3800000 read pairs finished. 657 secs passed Thread #3: 3850000 read pairs finished. 662 secs passed Thread #0: 3900000 read pairs finished. 663 secs passed Thread #7: 3950000 read pairs finished. 666 secs passed Thread #1: 4000000 read pairs finished. 667 secs passed Thread #4: 4050000 read pairs finished. 667 secs passed Thread #2: 4100000 read pairs finished. 669 secs passed Thread #6: 4150000 read pairs finished. 709 secs passed Thread #5: 4200000 read pairs finished. 714 secs passed Thread #0: 4300000 read pairs finished. 716 secs passed Thread #3: 4250000 read pairs finished. 717 secs passed Thread #7: 4350000 read pairs finished. 720 secs passed Thread #1: 4400000 read pairs finished. 722 secs passed Thread #4: 4450000 read pairs finished. 722 secs passed Thread #2: 4500000 read pairs finished. 723 secs passed Thread #6: 4550000 read pairs finished. 762 secs passed Thread #5: 4600000 read pairs finished. 768 secs passed Thread #0: 4650000 read pairs finished. 770 secs passed Thread #3: 4700000 read pairs finished. 771 secs passed Thread #7: 4750000 read pairs finished. 774 secs passed Thread #1: 4800000 read pairs finished. 776 secs passed Thread #4: 4850000 read pairs finished. 776 secs passed Thread #2: 4900000 read pairs finished. 778 secs passed Thread #6: 4950000 read pairs finished. 816 secs passed Thread #5: 5000000 read pairs finished. 822 secs passed Thread #0: 5050000 read pairs finished. 824 secs passed Thread #3: 5100000 read pairs finished. 825 secs passed Thread #7: 5150000 read pairs finished. 829 secs passed Thread #1: 5200000 read pairs finished. 830 secs passed Thread #4: 5250000 read pairs finished. 830 secs passed Thread #2: 5300000 read pairs finished. 832 secs passed Thread #6: 5350000 read pairs finished. 870 secs passed Thread #5: 5400000 read pairs finished. 876 secs passed Thread #0: 5450000 read pairs finished. 877 secs passed Thread #3: 5500000 read pairs finished. 879 secs passed Thread #7: 5550000 read pairs finished. 883 secs passed Thread #1: 5600000 read pairs finished. 885 secs passed Thread #4: 5650000 read pairs finished. 885 secs passed Thread #2: 5700000 read pairs finished. 886 secs passed Thread #6: 5750000 read pairs finished. 924 secs passed Thread #5: 5800000 read pairs finished. 930 secs passed Thread #0: 5850000 read pairs finished. 930 secs passed Thread #3: 5900000 read pairs finished. 933 secs passed Thread #7: 5950000 read pairs finished. 938 secs passed Thread #1: 6000000 read pairs finished. 939 secs passed Thread #4: 6050000 read pairs finished. 939 secs passed Thread #2: 6100000 read pairs finished. 941 secs passed Thread #6: 6150000 read pairs finished. 978 secs passed Thread #5: 6200000 read pairs finished. 984 secs passed Thread #0: 6250000 read pairs finished. 984 secs passed Thread #3: 6300000 read pairs finished. 987 secs passed Thread #7: 6350000 read pairs finished. 992 secs passed Thread #1: 6400000 read pairs finished. 993 secs passed Thread #4: 6450000 read pairs finished. 994 secs passed Thread #2: 6500000 read pairs finished. 995 secs passed Thread #6: 6550000 read pairs finished. 1031 secs passed Thread #5: 6600000 read pairs finished. 1038 secs passed Thread #0: 6650000 read pairs finished. 1038 secs passed Thread #3: 6700000 read pairs finished. 1041 secs passed Thread #7: 6750000 read pairs finished. 1046 secs passed Thread #1: 6800000 read pairs finished. 1047 secs passed Thread #4: 6850000 read pairs finished. 1048 secs passed Thread #2: 6900000 read pairs finished. 1050 secs passed Thread #6: 6950000 read pairs finished. 1085 secs passed Thread #5: 7000000 read pairs finished. 1091 secs passed Thread #0: 7050000 read pairs finished. 1092 secs passed Thread #3: 7100000 read pairs finished. 1096 secs passed Thread #7: 7150000 read pairs finished. 1100 secs passed Thread #1: 7200000 read pairs finished. 1102 secs passed Thread #4: 7250000 read pairs finished. 1102 secs passed Thread #2: 7300000 read pairs finished. 1105 secs passed Thread #6: 7350000 read pairs finished. 1139 secs passed Thread #5: 7400000 read pairs finished. 1145 secs passed Thread #0: 7450000 read pairs finished. 1145 secs passed Thread #3: 7500000 read pairs finished. 1150 secs passed Thread #7: 7550000 read pairs finished. 1155 secs passed Thread #1: 7600000 read pairs finished. 1156 secs passed Thread #4: 7650000 read pairs finished. 1157 secs passed Thread #2: 7700000 read pairs finished. 1159 secs passed Thread #6: 7750000 read pairs finished. 1193 secs passed Thread #5: 7800000 read pairs finished. 1199 secs passed Thread #0: 7850000 read pairs finished. 1199 secs passed Thread #3: 7900000 read pairs finished. 1204 secs passed Thread #7: 7950000 read pairs finished. 1209 secs passed Thread #1: 8000000 read pairs finished. 1210 secs passed Thread #4: 8050000 read pairs finished. 1211 secs passed Thread #2: 8100000 read pairs finished. 1213 secs passed Thread #6: 8150000 read pairs finished. 1247 secs passed Thread #5: 8200000 read pairs finished. 1253 secs passed Thread #0: 8250000 read pairs finished. 1254 secs passed Thread #3: 8300000 read pairs finished. 1259 secs passed Thread #7: 8350000 read pairs finished. 1263 secs passed Thread #1: 8400000 read pairs finished. 1265 secs passed Thread #4: 8450000 read pairs finished. 1265 secs passed Thread #2: 8500000 read pairs finished. 1268 secs passed Thread #6: 8550000 read pairs finished. 1301 secs passed Thread #5: 8600000 read pairs finished. 1307 secs passed Thread #0: 8650000 read pairs finished. 1307 secs passed Thread #3: 8700000 read pairs finished. 1313 secs passed Thread #7: 8750000 read pairs finished. 1317 secs passed Thread #1: 8800000 read pairs finished. 1319 secs passed Thread #4: 8850000 read pairs finished. 1320 secs passed Thread #2: 8900000 read pairs finished. 1323 secs passed Thread #6: 8950000 read pairs finished. 1355 secs passed Thread #5: 9000000 read pairs finished. 1361 secs passed Thread #0: 9050000 read pairs finished. 1361 secs passed Thread #3: 9100000 read pairs finished. 1368 secs passed Thread #7: 9150000 read pairs finished. 1371 secs passed Thread #1: 9200000 read pairs finished. 1373 secs passed Thread #4: 9250000 read pairs finished. 1374 secs passed Thread #2: 9300000 read pairs finished. 1377 secs passed Thread #6: 9350000 read pairs finished. 1409 secs passed Thread #5: 9400000 read pairs finished. 1415 secs passed Thread #0: 9450000 read pairs finished. 1415 secs passed Thread #3: 9500000 read pairs finished. 1422 secs passed Thread #7: 9550000 read pairs finished. 1425 secs passed Thread #1: 9600000 read pairs finished. 1427 secs passed Thread #4: 9650000 read pairs finished. 1428 secs passed Thread #2: 9700000 read pairs finished. 1432 secs passed Thread #6: 9750000 read pairs finished. 1463 secs passed Thread #5: 9800000 read pairs finished. 1469 secs passed Thread #0: 9850000 read pairs finished. 1470 secs passed Thread #3: 9900000 read pairs finished. 1477 secs passed Thread #7: 9950000 read pairs finished. 1480 secs passed Thread #1: 10000000 read pairs finished. 1482 secs passed Thread #4: 10050000 read pairs finished. 1482 secs passed Thread #2: 10100000 read pairs finished. 1486 secs passed Thread #6: 10150000 read pairs finished. 1517 secs passed Thread #5: 10200000 read pairs finished. 1523 secs passed Thread #0: 10250000 read pairs finished. 1524 secs passed Thread #3: 10300000 read pairs finished. 1531 secs passed Thread #7: 10350000 read pairs finished. 1534 secs passed Thread #1: 10400000 read pairs finished. 1536 secs passed Thread #4: 10450000 read pairs finished. 1536 secs passed Thread #2: 10500000 read pairs finished. 1540 secs passed Thread #6: 10550000 read pairs finished. 1570 secs passed Thread #5: 10600000 read pairs finished. 1576 secs passed Thread #0: 10650000 read pairs finished. 1576 secs passed Thread #3: 10700000 read pairs finished. 1584 secs passed Thread #7: 10750000 read pairs finished. 1587 secs passed Thread #1: 10800000 read pairs finished. 1589 secs passed Thread #4: 10850000 read pairs finished. 1590 secs passed Thread #2: 10900000 read pairs finished. 1593 secs passed Thread #6: 10950000 read pairs finished. 1623 secs passed Thread #5: 11000000 read pairs finished. 1629 secs passed Thread #0: 11050000 read pairs finished. 1630 secs passed Thread #3: 11100000 read pairs finished. 1637 secs passed Thread #7: 11150000 read pairs finished. 1640 secs passed Thread #1: 11200000 read pairs finished. 1642 secs passed Thread #4: 11250000 read pairs finished. 1643 secs passed Thread #2: 11300000 read pairs finished. 1646 secs passed Thread #6: 11350000 read pairs finished. 1676 secs passed Thread #5: 11400000 read pairs finished. 1682 secs passed Thread #0: 11450000 read pairs finished. 1684 secs passed Thread #3: 11500000 read pairs finished. 1690 secs passed Thread #7: 11550000 read pairs finished. 1694 secs passed Thread #1: 11600000 read pairs finished. 1695 secs passed Thread #4: 11650000 read pairs finished. 1695 secs passed Thread #2: 11700000 read pairs finished. 1699 secs passed Thread #6: 11750000 read pairs finished. 1729 secs passed Thread #5: 11800000 read pairs finished. 1735 secs passed Thread #0: 11850000 read pairs finished. 1737 secs passed Thread #3: 11900000 read pairs finished. 1743 secs passed Thread #7: 11950000 read pairs finished. 1748 secs passed Thread #1: 12000000 read pairs finished. 1748 secs passed Thread #4: 12050000 read pairs finished. 1749 secs passed Thread #2: 12100000 read pairs finished. 1753 secs passed Thread #6: 12150000 read pairs finished. 1782 secs passed Thread #5: 12200000 read pairs finished. 1787 secs passed Thread #0: 12250000 read pairs finished. 1789 secs passed Thread #3: 12300000 read pairs finished. 1796 secs passed Thread #7: 12350000 read pairs finished. 1801 secs passed Thread #1: 12400000 read pairs finished. 1802 secs passed Thread #4: 12450000 read pairs finished. 1802 secs passed Thread #2: 12500000 read pairs finished. 1806 secs passed Thread #6: 12550000 read pairs finished. 1835 secs passed Thread #5: 12600000 read pairs finished. 1840 secs passed Thread #0: 12650000 read pairs finished. 1842 secs passed Thread #3: 12700000 read pairs finished. 1849 secs passed Thread #7: 12750000 read pairs finished. 1855 secs passed Thread #1: 12800000 read pairs finished. 1855 secs passed Thread #4: 12850000 read pairs finished. 1856 secs passed Thread #2: 12900000 read pairs finished. 1859 secs passed Thread #6: 12950000 read pairs finished. 1887 secs passed Thread #5: 13000000 read pairs finished. 1893 secs passed Thread #0: 13050000 read pairs finished. 1894 secs passed Thread #3: 13100000 read pairs finished. 1902 secs passed Thread #7: 13150000 read pairs finished. 1907 secs passed Thread #0: 13412322 read pairs finished. 1907 secs passed Thread #1: 13200000 read pairs finished. 1908 secs passed Thread #4: 13250000 read pairs finished. 1908 secs passed Thread #2: 13300000 read pairs finished. 1909 secs passed Thread #6: 13350000 read pairs finished. 1914 secs passed Thread #5: 13400000 read pairs finished. 1915 secs passed Total number of aligned reads: pairs: 7921708 (59%) single a: 2760364 (21%) single b: 2429695 (18%) Done. Finished at Wed Jun 4 08:54:08 2014 Total time consumed: 1916 secs
#where is bsmap
bsmap="/Users/Shared/Apps/bsmap-2.74/"
#bsmap="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"
#genome
genome="/Users/Steven/Downloads/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa"
!python {bsmap}methratio.py -d {genome} -u -z -g -o /Volumes/web/cnidarian/YE_mix_22sm_methratio_out.txt -s {bsmap}samtools /Volumes/web/cnidarian/BiLar_YE_mix_t_22sm.sam
@ Wed Jun 4 08:57:20 2014: reading reference /Users/Steven/Downloads/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ... @ Wed Jun 4 08:57:56 2014: reading /Volumes/web/cnidarian/BiLar_YE_mix_t_22sm.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Jun 4 09:01:15 2014: read 10000000 lines @ Wed Jun 4 09:04:31 2014: read 20000000 lines @ Wed Jun 4 09:04:53 2014: combining CpG methylation from both strands ... @ Wed Jun 4 09:05:20 2014: writing /Volumes/web/cnidarian/YE_mix_22sm_methratio_out.txt ... @ Wed Jun 4 09:15:24 2014: done. total 14516650 valid mappings, 50167358 covered cytosines, average coverage: 1.58 fold.
!head /Volumes/web/cnidarian/YE_mix_22sm_methratio_out.txt
chr pos strand context ratio eff_CT_count C_count CT_count rev_G_count rev_GA_count CI_lower CI_upper C12706 112 + TTCTA 0.000 1.00 0 1 0 0 0.000 0.793 C12706 135 + GACTC 0.000 1.00 0 1 0 0 0.000 0.793 C12706 137 + CTCTT 0.000 1.00 0 1 0 0 0.000 0.793 C12706 148 + ATCAA 0.000 1.00 0 1 0 0 0.000 0.793 C12706 151 + AACTT 0.000 1.00 0 1 0 0 0.000 0.793 C12706 159 + AGCCT 0.000 1.00 0 1 0 0 0.000 0.793 C12706 160 + GCCTA 0.000 1.00 0 1 0 0 0.000 0.793 C12706 163 + TACAA 0.000 1.00 0 1 0 0 0.000 0.793 C12706 170 - AAGGT 0.000 1.00 0 1 2 2 0.000 0.793
#command for only obtaining the context '__CG_'
#!grep "[A-Z][A-Z]CG[A-Z]" </Volumes/web/cnidarian/YE_mix_22sm_methratio_out.txt> /Volumes/web/cnidarian/YE_mix_22sm_methratio_outCG.txt
#5x coverage
!awk '{if ($8 >= 3) print $1,$2-1,$2+1,"CpG",$5}' </Volumes/web/cnidarian/YE_mix_22sm_methratio_outCG.txt> /Volumes/web/cnidarian/YE_mix_22sm_outCG3x.igv
!tr ' ' "\t" </Volumes/web/cnidarian/YE_mix_22sm_outCG3x.igv> /Volumes/web/cnidarian/filt_YE_mix_22smCG3x.igv
!head /Volumes/web/cnidarian/filt_YE_mix_22smCG3x.igv
C12764 118 120 CpG 0.000 C12764 128 130 CpG 0.000 C12764 131 133 CpG 0.000 C12778 113 115 CpG 0.000 C12802 118 120 CpG 0.000 C12860 104 106 CpG 0.000 C12860 112 114 CpG 0.000 C12860 115 117 CpG 0.000 C12860 120 122 CpG 0.000 C12860 158 160 CpG 0.000