search

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
411 stars 118 forks source link

--gzipped-read-file should be --star-gzipped-read-file #102

Open xizhihui opened 6 years ago

xizhihui commented 6 years ago

We are told to use "--gzipped-read-file" in Examples( https://deweylab.github.io/RSEM/rsem-calculate-expression.html), however, "--star-gzipped-read-file" is the correct one.

tiagobrc commented 6 years ago

This took me 1-2 hours; I just made a long time to believe that the documentation was wrong/outdated.

RamRS commented 5 years ago

It's not just the documentation on the web that's wrong, the usage stuff output by running

rsem-calculate-expression 2>&1 | less -S

has internal inconsistencies.

This is the section of the usage doc describing the option: https://github.com/deweylab/RSEM/blob/master/rsem-calculate-expression#L982

And here is one of 4 examples using it wrongly (concordant with the web manual but discordant with the code): https://github.com/deweylab/RSEM/blob/master/rsem-calculate-expression#L1533

afaranda commented 4 years ago

The website still gives "--gzipped-read-file" as the option to use with gzipped read files. I'm glad I found this thread before spending a significant amount of time scratching my head!

http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html

RamRS commented 3 years ago

I think the WISC.edu website is outdated and the manual to be used is at https://deweylab.github.io/RSEM/

Google has the former indexed higher though, and that is a broken manual.