STAR output for downstream applications

[xbarvazx]

Dear all,

What is the recommended applications for using with STAR output?
I would like to try to use DESeq to analyze the expression between two samples after aligning with STAR.
What applications should be used? Do I use the '.sam' file for this?

Thanks,

[Alexander Dobin]

Hi,

the post-mapping applications depends on what your ultimate question is.

If you want to analyze differential expression with DEseq, you would need to calculate number of reads per gene in each sample.

Two popular software are HTseq and FeatureCount.

Cheers

Alex