Input BAM for RSEM

[Bekah W]

Hi,

I was wondering if anyone could confirm what parameters I need to specify when inputting my Aligned.toTranscriptome.out.bam file to RSEM please? 

I've been using:

rsem-calculate-expression 

--no-bam-output -

--bam -

-p 12 

--paired-end ./SampleA1_Aligned.toTranscriptome.out.bam 

./rsem_ref

./SA1_rsem_output

Do I need to specify "strandness"  as a stranded prep was used?

Best regards,
Bekah

[Alexander Dobin]

Hi Bekah,

you would need to specify strandedness with --forward-prob: 1 or 0 for stranded protocol.

Your other parameters look good.

Cheers

Alex

[Bekah W]

Thank you :)