%%bash
specifies to use the shell for this Jupyter cellfor file in /Volumes/nightingales/C_virginica/2112_lane1_[^N]*
initiates a for loop to handle all files beginning with 2212_lane2_
and only those that do not have the letter "N" at that position in the file name.do
tells the for loop what to do with each of the files.newname=${file##*/}
takes the value of the $file
variable (which is /Volumes/nightingales/C_gigas/2212_lane2_[^N]*
) and trims the longest match from the beginning of the pattern (the pattern is */
; the ##
is a bash command to specifiy how to trim). The resulting output (which is just the file name without the full path) is then stored in the newname
variable.SE
)-threads 16
),-phred33
),"$file"
),/Volumes/Data/Sam/scratch/20150414_trimmed_$newname
),ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10
),LEADING:3
)TRAILING:3
)SLIDINGWINDOW:4:15
)done
closes for loop.%%bash
for file in /Volumes/nightingales/C_virginica/2112_lane1_[^N]*
do
newname=${file##*/}
java -jar /usr/local/bioinformatics/Trimmomatic-0.30/trimmomatic-0.30.jar SE -threads 16 -phred33 "$file" /Volumes/Data/Sam/scratch/20150414_trimmed_$newname ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15;
done
TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ACAGTG_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 16000000 Surviving: 11370712 (71.07%) Dropped: 4629288 (28.93%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ACAGTG_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ACAGTG_L001_R1_002.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 1327210 Surviving: 889732 (67.04%) Dropped: 437478 (32.96%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ATCACG_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ATCACG_L001_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 16000000 Surviving: 13657433 (85.36%) Dropped: 2342567 (14.64%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ATCACG_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 16000000 Surviving: 13551447 (84.70%) Dropped: 2448553 (15.30%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ATCACG_L001_R1_003.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ATCACG_L001_R1_003.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 1409414 Surviving: 1173081 (83.23%) Dropped: 236333 (16.77%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_CAGATC_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_CAGATC_L001_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 16000000 Surviving: 12742235 (79.64%) Dropped: 3257765 (20.36%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_CAGATC_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_CAGATC_L001_R1_002.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 16000000 Surviving: 12468557 (77.93%) Dropped: 3531443 (22.07%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_CAGATC_L001_R1_003.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_CAGATC_L001_R1_003.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 7780221 Surviving: 6056165 (77.84%) Dropped: 1724056 (22.16%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_GCCAAT_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_GCCAAT_L001_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 16000000 Surviving: 13494573 (84.34%) Dropped: 2505427 (15.66%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_GCCAAT_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_GCCAAT_L001_R1_002.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 8792684 Surviving: 7316692 (83.21%) Dropped: 1475992 (16.79%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_TGACCA_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_TGACCA_L001_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 9188940 Surviving: 2827107 (30.77%) Dropped: 6361833 (69.23%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_TTAGGC_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 16000000 Surviving: 13428815 (83.93%) Dropped: 2571185 (16.07%) TrimmomaticSE: Completed successfully TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_TTAGGC_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Reads: 9752634 Surviving: 8034025 (82.38%) Dropped: 1718609 (17.62%) TrimmomaticSE: Completed successfully
%%bash
for file in /Volumes/Data/Sam/scratch/20150414_trimmed_2112*; do fastqc "$file" --outdir=/Volumes/Eagle/Arabidopsis/; done
Analysis complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_002.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_001.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_003.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_CAGATC_L001_R1_001.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_CAGATC_L001_R1_002.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_CAGATC_L001_R1_003.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_GCCAAT_L001_R1_001.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_GCCAAT_L001_R1_002.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001.fastq.gz Analysis complete for 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002.fastq.gz
Started analysis of 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 5% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 10% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 15% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 20% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 25% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 30% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 35% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 40% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 45% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 50% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 55% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz Approx 60% complete for 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20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 5% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 10% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 15% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 20% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 25% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 30% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 35% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 40% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 45% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 50% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 55% complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz Approx 60% complete for 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cd /Volumes/Eagle/Arabidopsis/
/Volumes/Eagle/Arabidopsis
%%bash
for file in 20150414_trimmed_2112_lane1_*.zip; do unzip "$file"; done
Archive: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc.zip creating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/ creating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/ creating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Images/ inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/fastqc_icon.png inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/warning.png inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/error.png inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/tick.png inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/summary.txt inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Images/per_base_quality.png inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Images/per_tile_quality.png inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Images/per_sequence_quality.png inflating: 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20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Icons/ creating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/ inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Icons/fastqc_icon.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Icons/warning.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Icons/error.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Icons/tick.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/summary.txt inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/per_base_quality.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/per_tile_quality.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/per_sequence_quality.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/per_base_sequence_content.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/per_sequence_gc_content.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/per_base_n_content.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/sequence_length_distribution.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/duplication_levels.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/adapter_content.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/Images/kmer_profiles.png inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/fastqc_report.html inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/fastqc_data.txt inflating: 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc/fastqc.fo Archive: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc.zip creating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/ creating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Icons/ creating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/ inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Icons/fastqc_icon.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Icons/warning.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Icons/error.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Icons/tick.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/summary.txt inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/per_base_quality.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/per_tile_quality.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/per_sequence_quality.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/per_base_sequence_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/per_sequence_gc_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/per_base_n_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/sequence_length_distribution.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/duplication_levels.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/adapter_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/Images/kmer_profiles.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/fastqc_report.html inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/fastqc_data.txt inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc/fastqc.fo Archive: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc.zip creating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/ creating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Icons/ creating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/ inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Icons/fastqc_icon.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Icons/warning.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Icons/error.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Icons/tick.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/summary.txt inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_base_quality.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_tile_quality.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_sequence_quality.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_base_sequence_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_sequence_gc_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_base_n_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/sequence_length_distribution.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/duplication_levels.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/adapter_content.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/kmer_profiles.png inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/fastqc_report.html inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/fastqc_data.txt inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/fastqc.fo
cd /Volumes/Data/Sam/scratch/
/Volumes/Data/Sam/scratch
%%bash
#gunzips all matching files in folder and appends the data to a single file:
#20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq
for file in 20150414_trimmed_2112_lane1_ATCACG*
do
gunzip -c "$file" >> 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq
done
%%bash
#Gzip file
gzip 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq
%%bash
#gunzips all matching files in folder and appends the data to a single file:
#20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq
for file in 20150414_trimmed_2112_lane1_TTAGGC*
do
gunzip -c "$file" >> 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq
done
%%bash
#Gzip file
gzip 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq
%%bash
#gunzips all matching files in folder and appends the data to a single file:
#20150414_trimmed_2112_lane1_HB30_Oil_25000ppm_TGACCA.fastq
for file in 20150414_trimmed_2112_lane1_TGACCA*
do
gunzip -c "$file" >> 20150414_trimmed_2112_lane1_HB30_Oil_25000ppm_TGACCA.fastq
done
%%bash
#Gzip file
gzip 20150414_trimmed_2112_lane1_HB30_Oil_25000ppm_TGACCA.fastq
%%bash
#gunzips all matching files in folder and appends the data to a single file:
#20150414_trimmed_2112_lane1_NB3_NoOil_ACAGTG.fastq
for file in 20150414_trimmed_2112_lane1_ACAGTG*
do
gunzip -c "$file" >> 20150414_trimmed_2112_lane1_NB3_NoOil_ACAGTG.fastq
done
%%bash
#Gzip file
gzip 20150414_trimmed_2112_lane1_NB3_NoOil_ACAGTG.fastq
%%bash
#gunzips all matching files in folder and appends the data to a single file:
#20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq
for file in 20150414_trimmed_2112_lane1_GCCAAT*
do
gunzip -c "$file" >> 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq
done
%%bash
#Gzip file
gzip 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq
%%bash
#gunzips all matching files in folder and appends the data to a single file:
#20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq
for file in 20150414_trimmed_2112_lane1_CAGATC*
do
gunzip -c "$file" >> 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq
done
%%bash
#Gzip file
gzip 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq
%%bash
for file in 2015*e1_[NH]B*; do cp "$file" /Volumes/Eagle/Arabidopsis/; done