Questions tagged [fastq-dump]

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3 votes
1 answer

Error output in nextflow pipeline using fasterq-dump

I have one file with multiple SRA accession called Dataframe_with_accession.txt, for this example I just put one SRA in that file called :...
1 vote
1 answer

How to split FASTQ reads without re-running `fastq-dump`?

I downloaded a few FASTQs from the SRA that were paired-end 76 bp. When I look at the FASTQs, I get something like this: ...
0 votes
2 answers

Using variables with fasterq-dump?

I am trying to download multiple fastq files from the SRA NCBI database which, conveniently enough, have their IDs in a range. Building a simple loop doesn't seem to do the trick, as bash appears to ...