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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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convert-sam-for-rsem documentation inconsistency #95

Open map2085 opened 6 years ago

map2085 commented 6 years ago

There is an inconsistency between RSEM online documentation and the binary utility man page for convert-sam-for-rsem.

The RSEM website documentation for rsem-calculate-expression says that convert-sam-for-rsem only accepts SAM format:

One simple way to make the alignment file satisfying RSEM's requirements (assuming the aligner used put mates in a paired-end read adjacent) is to use 'convert-sam-for-rsem' script. This script only accept SAM format files as input. If a BAM format file is obtained, please use samtools to convert it to a SAM file first.

however, the man page obtained via:

./convert-sam-for-rsem -h

says that BAM or SAM is allowed.