getting paired end datasets from SRA
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2.7 years ago

I am searching SRA by keywords like "paired-end", but the sra-toolkit seems to only download one file (single-end) about 90% of the time. I just want to make sure my commands are all correct:

prefetch SRR13310323
fastq-dump -I --split-files --outdir fastq --gzip --skip-technical  --readids --read-filter pass --dumpbase --split-3 --clip ~/ncbi/public/sra/SRR13310323.sra

The SRA entry says "Layout: PAIRED". It's totally possible that whoever uploaded entered incorrect metadata, but the SRA curation step could easily have validated whether it was paired-end or not, and generally prevented a lot of grief. so am i missing something in my command? can i filter my search in SRA differently to get the desired accession numbers?

NCBI SRA • 1.3k views
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Entering edit mode

'99% of the time', this works 'all the time':

fastq-dump --split-files SRR13310323

It will download anything there on the record. I then prefer to inspect the files and retain whatever I need. It should split reads into R1 and R2

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