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  • rsem: using genome bam for calculating expression

    Hello, I have run:
    rsem-calculate-expression
    on pair end sequencing. From the resulting BAM file mapped to the genome (sample.STAR.genome.bam), I would like to use that as an input to calculate expression of genes in the sample (actually a subset of it derived from filtering reads). I can try remapping, or any solution would work.
    When I try to use it as input in rsem-calculate-expression, it fails because the chromosome entries dont appear as a reference sequence( expected). Any help is appreciated!

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