Question: Paired-end SRA data comes out as a Single-end
0
gravatar for tjdrnjsqpf
6 months ago by
tjdrnjsqpf0
tjdrnjsqpf0 wrote:

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?

rna-seq software error • 304 views
ADD COMMENTlink modified 6 months ago by Devon Ryan80k • written 6 months ago by tjdrnjsqpf0

SRR87406 is not part of this dataset. Did you mean SRR870466?

ADD REPLYlink modified 6 months ago • written 6 months ago by WouterDeCoster29k

oops.. Yes it is typo. I fixed it.

ADD REPLYlink modified 6 months ago • written 6 months ago by tjdrnjsqpf0
1
gravatar for Devon Ryan
6 months ago by
Devon Ryan80k
Freiburg, Germany
Devon Ryan80k wrote:

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.

ADD COMMENTlink written 6 months ago by Devon Ryan80k
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