Lukas Käll

I added support for a filename column for tab delimited input and output. If percolator detects a column named "filename" in input, it will carry over its content to output...

The first two columns are reserved for id and labels. Placing the filename in column 3 or 4 seems to work well: $ ./percolator make-pin.txt 2> /dev/null | grep -q...

Hmm, which result in which article is it that you want to reproduce? On Wed, Jun 29, 2022 at 10:21 AM zerohuwan ***@***.***> wrote: > Hello, I want to reproduce...

I see. The datasets are available here: https://noble.gs.washington.edu/proj/percolator/ The software has evolved significantly since its release. Particularly, you need to run sqt2pin in order to use sqt files. --Lukas On...

Thank you for reporting the error. Would you be able to share the dataset you used when the problem occurred? --Lukas On Thu, May 19, 2022 at 12:23 PM micgrab...

Right! You need to install a package containing msgf2pin, e.g. percolator-converters-xxx.yyy

Hi Miguel, It seems like there is something going on with the peptide or protein names. Would you be able to paste the first couple of rows of the file...

Thanks for your reply. Yes, some of the peptides are missing, i.e. there is only a _. in the peptide column. For the same rows there is no protein name...

Yes, percolator selects one of the three CV directions as the init direction. We set it up so that it always selects the first one.

This sounds like a problem with arch's byuld of codesynthesis/xsd rather than the cmakefile. Could you try building xsd youself according to these instructions? https://www.codesynthesis.com/projects/xsd/extras/build-unix.xhtml Thanks! --Lukas On Sun, Feb...