Question: How to get counts of STAR output (sam/bam).
0
gravatar for Shahzad
2.9 years ago by
Shahzad10
Pakistan
Shahzad10 wrote:

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 alignment assembly genome • 6.3k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Shahzad10
2
gravatar for Michael Dondrup
2.9 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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.

ADD COMMENTlink modified 23 months ago • written 2.9 years ago by Michael Dondrup46k
2

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

ADD REPLYlink written 2.9 years ago by genomax67k

thank you dear @Michael Dondrup.

ADD REPLYlink written 2.9 years ago by Shahzad10
1
gravatar for Irsan
2.9 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

HTseq is another popular option

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Irsan6.8k
1

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.

ADD REPLYlink written 2.9 years ago by Ar830

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

ADD REPLYlink written 2.9 years ago by Irsan6.8k
0
gravatar for Shahzad
2.9 years ago by
Shahzad10
Pakistan
Shahzad10 wrote:

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

ADD COMMENTlink written 2.9 years ago by Shahzad10
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