Different files with SRA Explorer and SRA toolkit fasterq-dump
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7 months ago

Greetings community

I'm currently processing public datasets from my species of interest. One of my samples, which I thought was PE came back as SE after I downloaded using SRA Explorer. I thought this was weird and I double-checked in NCBI and my sample is indeed supposed to be pair-ended. I tried to download using fasterq-dump and I was able to obtain the 2 files.

(here is the sample in question)

I'm not sure if this is a bug in SRA explorer or it might just be a badly annotated submission. Can anyone explain the different results? Thanks in advance

SRA_Explorer SRA-toolkit • 465 views
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It may be incorrectly annotated. If paired-end, the two reads are submitted interleaved or worse two files concatenated end-to-end.

When you go to the traces listing at NCBI it shows one read (LINK). EBI-ENA predictably has a single file for download as well.

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My first hypothesis was that the PE reads were deposited in the same file but after download, the single fastq file from SRA explorer was around 1.6G, while downloading using fasterq-dump I got two files, each with 1.5G. Also the NCBI listing shows 2 reads not 1

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Take a look at NCBI traces site link I posted above which shows one read. If you inspect actual reads under the "Read" tab those appear to be ~100bp each. It may be best to check the publication associated with the data (and/or contact submitters) to be sure.

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