Hi,
I want to calculate exon counts from a large number of bam files. I have done this before using HTseq. Since I have a large number bam files I really need to make this process as efficient as possible. Which programs would you recommend?
I am using cloud resources with multiple CPUs.
•
written
by
lkmklsmn
Just invoke multiple instances of htseq-count, one per file. I routinely count all of my samples at once that way. Allegedly featureCounts from subread is faster, but I've not used it.
featureCounts is really fast. It usually takes less than a minute per sample (which obviously depends on the size of the sample). That said, I still use HTSeq out of habit because it's fast enough.
Good to hear from someone who's used featureCounts (and isn't its author) that it really is that fast! Was it relatively straight-forward to get working?
Yes, I had no problems getting it to run. I have been using it in R through the Rsubread package, pretty much following the manual.
I'll second the sentiment that featureCounts is a nice speed increase.
Log in to answer this question.
