How to tell if GEO SRA is paired or single?
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Entering edit mode
12 weeks ago
simplitia ▴ 120

Hi, I'm trying to download data from the geo website using the sra toolkit. I'm interested in this sample here,

https://www.ncbi.nlm.nih.gov/sra/SRR6826132

However I can't make out if this is single or paired?

fastq-dump --outdir /N/p/lab.mis/elliot/bulk/raw_ext_JEM/raw/ --gzip --split-files SRR6826132


however this only resulted in single fastq file, SRR6826132_1.fastq.gz

is there way I can make sure that this is indeed sing and not paired? I can't find the info. thanks in advance. .

rnaseq geo • 385 views
2
Entering edit mode
12 weeks ago
GenoMax 125k

Looks like it is single end (relevant section posted).

\$ efetch -db sra -id SRR6823132 -format docsum

<LIBRARY_LAYOUT>
<SINGLE/>
</LIBRARY_LAYOUT>

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Entering edit mode

thanks; I saw the "layout" and was wondering what 'single' actually means.

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Entering edit mode
12 weeks ago

Without using the command line you can do this in a web browser.

Note it states:

Layout: SINGLE

On the page of the link you provided.

To be sure you can click on the link titled SRR6826132under Runs. You can see a visualization of the reads (note it says 0% R2) on this page and also if you click the tab Reads and you should be able to see your breakdown. You can check the box technical reads to double check that the second read isn't accidentally hidden or something.

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Entering edit mode

good point thank you. The "Layout" nomenclature threw me off.