RSEM

Prepare reference sequences

$ rsem-prepare-reference my_fasta.fa my_fasta.rsem

Convert SAM file

Convert my_result.sam to my_result.rsem.bam

$ convert-sam-for-rsem my_result.sam my_result.rsem 2>rsem.convert.log

Calculate expression (single-end)

(output of convert-sam-for-rsem) (reference) (output name)

$ rsem-calculate-expression --bam my_result.rsem.bam my_fasta.rsem my_result.rsem 2>rsem.calc.log

Calculate expression (paired-end)

(output of convert-sam-for-rsem) (reference) (output name)

$ rsem-calculate-expression --paired-end --bam my_result.rsem.bam my_fasta.rsem my_result.rsem 2>rsem.calc.log

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