Cuffmerge assemblies on pre and post intervention ?

[muehlsch]

I have RNA-seq data on pre and post intervention. 24 patient samples pre, and then 24 patient samples after the intervention. I will be performing a cuffdiff analysis looking at difference between pre vs. post, but also at different phenotypes.

Should I use cuffmerge to merge just the pre gtf files, or should I put both the pre and post into the assemblies files together, knowing that the post samples are from the same patients (but post intervention).

Thanks for any insight.

[muehlsch]

Cuffmerge assemblies on pre and post intervention ? - f/u

I should mention since it might not be clear - the pre and post samples are from the same patients. So pre sample gets taken from patient 1 > intervention > post sample from that patient. The same deal with patient 2,... and so on.

[DZhang]

If the nature and time course of your intervention are expected to generate new splicing variants or transcripts, you should merge both pre and post gtfs.

Best regards,
Douglas

https://www.contigexpress.com