Sam input to RSEM

[mtiwaridros]

Hi

I want to use rsem-calculate-expression on sam files (that I generated using STAR).
I checked for the validity of these sam files using

rsem-sam-validator <input.sam/input.bam>

and the results for all the sam files says

The input file is valid!

Now I use this sam file to feed to rsem-calculate-expression using:

rsem-calculate-expression --paired-end --sam --p 8 /Home/RSEM Sample1Aligned.out.sam /Home/RSEM/Expr Bam1quals

But cannot get it to run. It says:

Invalid number of arguments!

Can someone please indicate the problem.

Thanks.

Best
M

[dpryan]

Are you actually using "--p 8"? Try "-p 8" and see if that solves the problem (it should, at least from looking at the source code).