inconsistent results of rsem quantification

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

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inconsistent results of rsem quantification #122

Open gnilihzeux opened 5 years ago

gnilihzeux commented 5 years ago

I find rsem-calculate-expression put out two different results after my twice running with default parameters.
I use the bowtie2 aligner and foud parameter -k will search for one or more alignments and RSEM has a default set --bowtie2-k 200.
So, I guess that rsem will assign multiple alignment reads randomly.
Anyone suffers this ?