How To Merge Cuffdiff (Gene_Exp.Diff) Results From Two Batches Or Rnaseq Data?

Question

[newDNASeqer]

I have two batches of RNA Seq data. The first batch was done months ago, and I just finished the second batch and need to merge it with the previous cuffdiff results. Is there any easier way than re-running the previous data with the newer batch through Cuffmerge? thanks

Answer 1

[seidel]

You may need to supply more detail, as it's not clear what you mean by batches and how they relate to each other. However, when you mention cuffdiff results and cuffmerge next to each other, it implies that your first batch was used to generate transcript descriptions along with quantification and comparison (i.e. cuffdiff) between samples, and that you did not supply an external GTF file of transcript descriptions. Now that you have a second batch of data, if you want to quantify it in relation to the first batch, you would run the pipeline with the GTF file based on your first batch.

However, given that you now have more data, it's likely that if you combined your first and second batches, and ran everything again, your transcript descriptions would change slightly (thus the need for cuffmerge). So you have to decide what it is your are quantifying. If your goal is to use your data to generate transcript descriptions, then you should run everything again, use cuffmerge to generate a single set of GTF transcript descriptions, then run everything on that set of transcript descriptions, and you will have quantitative and comparison data on a uniform set of transcripts based on both batches.