Genome = Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa
GTF = Crassostrea_gigas.GCA_000297895.1.21.gtf
#Sample name
id="BB3"
#iget command with bam output from Tophat (genome Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa; gtf Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa)
ig="
Set working directory
cd /Volumes/web/cnidarian/qdod2/RNAseq
/Volumes/web/cnidarian/qdod2/RNAseq
!mkdir {id}
#downloading bam file
!{ig}
!samtools sort /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.bam /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.sorted
[bam_sort_core] merging from 18 files...
!head /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa
>C12728 dna_sm:supercontig supercontig:GCA_000297895.1:C12728:1:200:1 TTTTTCTTATTTTTATTTGTACCAGTTAATCCTGTGAgccgcttttatgtctctttctgg ccgtttttatgtctctttctgTTGACTTTATTATTCTCTCATTTATGATTTAACATCTCA TATGAATTATTATGTGTATCTTGCATGGGATATTTTGCCACTTCGTGCCCATAAAAATCA ACACTTGTCTTTCGGTGTAT >C12722 dna_sm:supercontig supercontig:GCA_000297895.1:C12722:1:200:1 TAGGGACAGTGTCTATTGCATTAAGGTGAGTGACTGTTTGGGGTTAAACTTAAACAGGTA TGGATAGATTGAGTGTGTGAACATCCCTGCTCTATCTAATCTACGTGTTTTCTAACCTTT GATACAAAGTGTGCGGTCATTCCTGCCCTGTATCGCATTAATACAAGTGTGCAGTCATAC CTGCTTGTATTGGTGGTGGT
!perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)} print $_;} print "\n"; warn "\nConverted $count FASTA records in $. lines to tabular format\nTotal sequence length: $len\n\n";' /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa > /Volumes/web/cnidarian/cgigasgenome1.tab
Converted 7658 FASTA records in 9306685 lines to tabular format Total sequence length: 557717710
!perl -e '$col = 2;' -e 'while (<>) { s/\r?\n//; @F = split /\t/, $_; $len = length($F[$col]); print "$_\t$len\n" } warn "\nAdded column with length of column $col for $. lines.\n\n";' /Volumes/web/cnidarian/cgigasgenome1.tab > /Volumes/web/cnidarian/cgigasgenome2.tab
Added column with length of column 2 for 7658 lines.
!awk '{ print $1,$5 }' /Volumes/web/cnidarian/cgigasgenome2.tab > /Volumes/web/cnidarian/cgigasgenome3.tab
!tail /Volumes/web/cnidarian/cgigasgenome3.tab
scaffold77 1619719 scaffold337 1638316 scaffold86 1697160 scaffold1532 1715538 scaffold419 1725835 scaffold102 1727112 scaffold1024 1774716 scaffold150 1854615 scaffold1009 1861391 scaffold22 1964558
RNA-Seq DH3; pooled gill, Drayton Harbor
!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -s "set rowcount 10 SELECT * FROM [sr320@washington.edu].[RNA-Seq_DH3]" -f tsv -o /Volumes/web/cnidarian/pDOD_DH3.txt
!head -4 /Volumes/web/cnidarian/pDOD_DH3.txt