Create pseudo-replicates by "evenly" splitting reads file?
0
0
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
ADD COMMENT
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1695 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6