danielecook
1/28/2016 - 11:45 PM

Extract fasta sequences from CDS #fasta

Extract fasta sequences from CDS #fasta

exon_file="N2_GFF_WS245/CDS.gff.gz"
reference="reference/c_elegans.PRJNA13758.WS245.genomic.fa"
paste <(gunzip -kfc ${exon_file})  <(bedtools getfasta -fi ${reference} -bed ${exon_file} -tab -fo -) | grep 'WormBase'