Paired-end SRA data comes out as a Single-end
I tried to download RNA-Seq data with accession SRX286028 (NCBI SRA data). It is Paired-end dataset and has multiple runs files (SRR870465, SRR870466, SRR870467, SRR870507, SRR870508, SRR870509, SRR870516, SRR870522, SRR870524, SRR870525).
And I decompressed all to forward and reverse files with "--split-3" sra-toolkit parameters.
All samples were split into 2 files (forward and reverse) successfully except SRR874066. It was split into a single .fastq file.
Is there a problem with the data or my sra-toolkit parameter?
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Devon Ryan
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tjdrnjsqpf •
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tjdrnjsqpf •
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It looks like the data was uploaded like that, so there's nothing you can do on your end to reliably change that. My guess is that there were issues with read #2.
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SRR87406is not part of this dataset. Did you mean SRR870466?oops.. Yes it is typo. I fixed it.