Open Koen-vdl opened 3 years ago
Thanks for this great resource. fastqc-dump is fairly poorly documented so this workbook was a great starting point for me.
fastqc-dump
I think there is a small error on: https://bioinformaticsworkbook.org/dataAcquisition/fileTransfer/sra.html#gsc.tab=0
parallel --jobs 3 "fastq-dump --split-files --origfmt --gzip {}" ::: SRR.numbers
I believe this will only work if you catSRR.numbers
cat
parallel --jobs 3 "fastq-dump --split-files --origfmt --gzip {}" ::: $( cat SRR.numbers)
Yes, $( cat SRR.numbers) would work, or you can use four colons instead of three (as just now suggested in pull request #60).
Thanks for this great resource.
fastqc-dump
is fairly poorly documented so this workbook was a great starting point for me.I think there is a small error on: https://bioinformaticsworkbook.org/dataAcquisition/fileTransfer/sra.html#gsc.tab=0
parallel --jobs 3 "fastq-dump --split-files --origfmt --gzip {}" ::: SRR.numbers
I believe this will only work if you
cat
SRR.numbersparallel --jobs 3 "fastq-dump --split-files --origfmt --gzip {}" ::: $( cat SRR.numbers)