Difference between revisions of "RSEM"
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$ convert-sam-for-rsem my_result.sam my_result.rsem 2>rsem.convert.log | $ convert-sam-for-rsem my_result.sam my_result.rsem 2>rsem.convert.log | ||
| − | == Calculate expression == | + | == Calculate expression (single-end) == |
(output of convert-sam-for-rsem) (reference) (output name) | (output of convert-sam-for-rsem) (reference) (output name) | ||
| − | $ rsem-calculate-expression my_result.rsem.bam my_fasta.rsem my_result.rsem 2>rsem.calc.log | + | $ 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 | ||
---- | ---- | ||
[[Category:HowTo]] | [[Category:HowTo]] | ||
Latest revision as of 13:26, 12 January 2015
Contents
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
