Question: Confusion with 2nd Read pair SRA download
0
gravatar for jaqx008
5 months ago by
jaqx00870
jaqx00870 wrote:

Hello everone. I am trying to download an RNAseq data from ncbi. the data layout shows the reads are paired end. if I understand correctly, that means I will need to download two fastq files m1 and m2. However, if I open the link, i see 4 runs which I assume is the m1. How do I find the m2 please? I plan on using this with bowtie2. see ascession number below

SRX5972887

Thanks

paired reads fastq sra • 169 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by jaqx00870
2
gravatar for genomax
5 months ago by
genomax78k
United States
genomax78k wrote:

Post the accession number so people can offer informed advice. As recommended, get fastq data directly from EBI-ENA whenever possible.

These are paired-end data there are 4 submissions (each with a pair of files).

ADD COMMENTlink modified 5 months ago • written 5 months ago by genomax78k

Thank you I see it now on EBI-ENA

ADD REPLYlink written 5 months ago by jaqx00870
1

Metadata looks the same for all 4 so it is possible that they submitted 4 lanes from a single NextSeq 550 flowcell as independent submissions.

ADD REPLYlink written 5 months ago by genomax78k
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