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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Using STAR BAMs from genomic alignment #210

Closed charlesdavid closed 4 months ago

charlesdavid commented 4 months ago

Wanted to try this program with my existing alignment files to a genome. Ran the preprocessing and got all the indices, but looks like this code can not handle what I want to do. Could someone tell me how to proceed or that it is not possible? Thanks. (All most all of our work uses genomic alignments with STAR. So need to know if our workflows are compatible with RSEM) :-)

pliu55 commented 4 months ago

@charlesdavid RSEM's rsem-calculate-expression has an option --bam that can use STAR BAMs. Note that, this BAM needs to be alignment on transcriptome, not genome.

charlesdavid commented 4 months ago

Right. So NOT compatible with genomic alignments. Oh well.