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1 vote
2 answers
2k views

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: ...
1 vote
1 answer
71 views

Downloading multiple SRA files as FASTQ files using SRA Toolkit

I was able to download all of the SRA files for a specific bioproject using the command: prefetch -O output_directory --option-file SRR_Acc_List.txt I then tried ...
3 votes
1 answer
145 views

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 :...
0 votes
2 answers
237 views

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 ...