Calculating Fpkm/Rpkm For Each Read Group Given A Gtf File

Question

[Nathan S. Watson-Haigh]

I have a couple of BAM files, each containing several read groups, and an associated GTF file. I'd like to calculate the FPKM/RPKM's for each transcript for each read group. One of the files is from single-end reads, the other from paired-end reads.

Is there an existing tool that can calculate the FPKM/RPKMs for each individual read group in a BAM file?

[Michael]

You need a way of identifying the read groups, are they annotated in the BAM file (should use @RG tag). Samtools has the -R/r parameters:

-R FILE  list of read groups to be outputted [null]
-r STR   only output reads in read group STR [null]

maybe that can be used to produce a set of BAM files for which to calculate FPKM separately?

[Ashutosh Pandey]

I don't know of any tool that can do it at the read group level, if your bam file contains several read groups. You will have to separate the big bam into several small ones (one for each read group) and process them individually.