--OutFileNamePrefix

[Varun Gupta]

Hi Alex,
I want to report out my alignment files with the prefix name

I provided the star run with --outFileNamePrefix brain

The resulting files produced were

brainAligned.out.sam
brainLog.out
brainLog.progress.out

Can I just get output like brain.sam(Only interested in sam format as of now).

Regards
Varun

[Alexander Dobin]

Hi Varun,

unfortunately, this is just the name prefix, you cannot change the suffix. 

You could use --outStd SAM option, and re-direct the stdout to brain.sam file:

$ STAR ...  --outStd SAM ... > brain.sam

Another option is to simply sym-link brain.sam to Aligned.out.sam

Cheers

Alex