Hi Everyone,
I wanted to find out if it is possible to supply Cuffmerge with more input files than are going to be used in Cuffdiff for differential expression analysis.
For example: Can I supply Cuffmerge with all 8 of my sample assemblies, and a reference genome to create a merged assembly, but then when I perform Cuffdiff analysis, can I examine the differential expression of only a subset (say 2) of those 8 files? Will having the extra information in the merged assembly cause an incorrect expression analysis?
Or, alternatively, do I need to only merge those 2 samples with the reference annotation in Cuffmerge, to examine only those 2 files using Cuffdiff?
Thanks for your help!
I wanted to find out if it is possible to supply Cuffmerge with more input files than are going to be used in Cuffdiff for differential expression analysis.
For example: Can I supply Cuffmerge with all 8 of my sample assemblies, and a reference genome to create a merged assembly, but then when I perform Cuffdiff analysis, can I examine the differential expression of only a subset (say 2) of those 8 files? Will having the extra information in the merged assembly cause an incorrect expression analysis?
Or, alternatively, do I need to only merge those 2 samples with the reference annotation in Cuffmerge, to examine only those 2 files using Cuffdiff?
Thanks for your help!