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