Question

Merging 2 SRR runs of the same sample?

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2.3 years ago

osiemen ▴ 30

Hi, I know that there are previously been asked questions asked related to this question, but im still a bit confused. I have the following Sample SRX5486117 which contains 2 illumina runs. So this will give me 4 fastq files in total. Im not sure whether this is a biological or technical replicate and whether I should merge the 2 SRR runs. Is there a way to know this?

Thanks a lot!

SRA Sample RNA-Seq SRX SRR • 1.2k views

ADD COMMENT • link updated 2.3 years ago by ATpoint 85k • written 2.3 years ago by osiemen ▴ 30

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Both SRR files are the exact replicate: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127942, the Sample GSM3656922. You are expecting more than 30 million reads per sample.

ADD REPLY • link 2.3 years ago by zorbax ▴ 650

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So does this mean I should/could use both of them separately in my analysis? I understand that these are technical replicates. Even-though the fastq files wont be exactly the same right?

ADD REPLY • link 2.3 years ago by osiemen ▴ 30

score 0 · Answer 1 · 2022-08-19

There is no save way to tell whether several SRR files are biological or technical replicates, I've seen examples for both. Since in this case the authors seem to have properly organized samples (https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=525843) I guess it is a sequencing / technical replicate so I would simply cat together the two R1 and R2 files respectively prior to alignment / quantification.