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

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

rna-seq rna-seq alignment assembly genome
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written by Shahzad • Shahzad

3 answers

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.

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written by Michael Dondrup Michael Dondrup

thank you dear @Michael Dondrup.

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written by Shahzad • Shahzad

HTseq is another popular option

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written by Irsan Irsan

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.

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written by ATRX ATRX

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

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written by Irsan Irsan

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

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written by Shahzad • Shahzad

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