Question: Paired-end SRA data comes out as a Single-end
1
gravatar for tjdrnjsqpf
2.5 years ago by
tjdrnjsqpf10
tjdrnjsqpf10 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 • 1.1k views
ADD COMMENTlink modified 2.5 years ago by Devon Ryan95k • written 2.5 years ago by tjdrnjsqpf10

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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by WouterDeCoster43k

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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by tjdrnjsqpf10
2
gravatar for Devon Ryan
2.5 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k 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 2.5 years ago by Devon Ryan95k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1306 users visited in the last hour