danielecook
2/10/2016 - 4:53 PM

fetch stuff from sra #fastq

fetch stuff from sra #fastq

sra_fetch.sh
content_copyfile_download
esearch -db sra -query PRJNA40075  | efetch --format runinfo | cut -d ',' -f 1 | grep SRR > seqs.tsv

while read p; do
  fastq-dump --split-files --gzip $p
done <../seqs.tsv