Is it possible to use RSEM with BAM files from STAR alignment?

Question

[knowNot]

I am trying to use RSEM for quantification of expression levels and the files I have are BAM from STAR alignments. Would I need to run both "rsem-prepare-reference" and "rsem-calculate-expression" for this, or is the latter sufficient? Secondly, what are the options I need for successfully running these calculations?

I am very new to computational methods, please do excuse the naivete of my dilemma.

Thanks!

Answer 1

[Thind amarinder]

I know, it's late reply. But yes, this is possible. Here is something I got from STAR manual (https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf).

"6 Output in transcript coordinates. With --quantMode TranscriptomeSAM option STAR will output alignments translated into transcript coordinates in the Aligned.toTranscriptome.out.bam file (in addition to alignments in genomic coordinates in Aligned.*.sam/bam files). These transcriptomic alignments can be used with various transcript quantification software that require reads to be mapped to transcriptome, such as RSEM or eXpress. For example, RSEM command line would look as follows:

rsem-calculate-expression ... --bam Aligned.toTranscriptome.out.bam
/path/to/RSEM/reference RSEM

. Note, that STAR first aligns reads to entire genome, and only then searches for concordance between alignments and transcripts. I believe this approach might offer certain advantages compared to the alignment to transcriptome only, by not forcing the alignments to annotated transcripts. By default, the output satisfies RSEM requirements: soft-clipping or indels are not allowed. Use --quantTranscriptomeBan Singleend to allow insertions, deletions ans soft-clips in the transcriptomic alignments, which can be used by some expression quantification software (e.g. eXpress)."