Masking abundant sequences (hg19) when running Cuffdiff

[sindrle]

Hi!

I want to look for changes in mRNA "before" and "after" an intervention. I only use one patient (two time point) for this test.

I have two .BAM files from Tophat2.

When I use cuffdiff, how can I mask all abundant sequences in hg19? I have hg19 from iGenomes and in the "abundant sequences" there are alot of FASTA files.

Pls help, thank you!

[sindrle]

I guess the answer is to use chromosomes.fasta from hg19. Use the only ones youll like (not i.e. ChrM). Merge them as a new fast file and use that one as reference genome.

Cheers!