Create pseudo-replicates by "evenly" splitting reads file?
Entering edit mode
5 months ago
Dunois ★ 1.3k

So I have an RNA-seq dataset that should have been sequenced as three separate replicates (per condition) that got sequenced as one sample per condition for reasons. The data are paired-end.

This, I suppose, means (in theory) that I would not be able to do any differential gene expression analysis using this data. But I would love for the data not to go to waste.

Is there any way now that I could take the reads files R1 and R2 for each condition and create: pseudoreplicate1_R1 & pseudoreplicate1_R2

pseudoreplicate2_R1 & pseudoreplicate2_R2

pseudoreplicate3_R1 & pseudoreplicate3_R2

such that each the reads from R1 and R2 are uniformly (evenly?) represented in their subsets pseudoreplicate[1-3]_R[1-2]?

If not, are there any other suggestions for dealing with this scenario? In specific, I must mention that this data is/was intended for a time-series/time-course analysis.

RNA-Seq Assembly paired-end reads • 222 views
Entering edit mode

They will simply become technical/sequencing replicates after split. Nothing is going to change that.


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