How to get counts of STAR output (sam/bam).

Question

[Shahzad]

Dear Members I am working on RNA-seq differential expression. I have aligned my RNA reads on reference genome using STAR. I need to know to get counts from the output files of STAR OR how to get the count table in RStudio for further analysis. What other options do I have if I don't use cufflinks/cuffdiff.

THANKS

Answer 1

[Michael]

STAR 2.5 can now produce the counts directly using --quantMode, see https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf - Section 7, pp. 14ff

There are other programs like FeatureCounts, and Bioconductor packages, Edit: due to bad experiences I removed the recommendation for easyRNASeq.

[GenoMax]

featureCounts is also available as part of the R subread package.

[Shahzad]

thank you dear @Michael Dondrup.

Answer 2

[Irsan]

HTseq is another popular option

[ATRX]

I compared the numbers between the HTSeq and quantMode from STAR and the output is pretty much the same. The upside is STAR is much faster than tophat+htseq. Although, my experience has been with smaller sample set but even the authors claim that the counts coincide with those produced by htseq-count with default parameters.

[Irsan]

Hmm I still use star + htseq. I need to update my star version

Answer 3

[Shahzad]

Thank you all for your help. It solved my problem.