Questions tagged [fastq-dump]
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4 questions
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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 ...
- 13
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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 :...
- 155
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2
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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 ...
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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:
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