Difference between revisions of "RSEM"
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TaejoonKwon (Talk | contribs) (Created page with "== Prepare reference sequences == $ rsem-prepare-reference my_fasta.fa my_fasta.rsem == Convert SAM file == ---- Category:HowTo") |
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== Convert SAM file == | == 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 == | ||
| + | (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 | ||
| + | |||
---- | ---- | ||
[[Category:HowTo]] | [[Category:HowTo]] | ||
Revision as of 13:10, 12 January 2015
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
(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
