#429 Percolator does not report all of the PSMs

[William S Noble]

It appears that Crux Percolator does not report as many PSMs as the corresponding stand-alone version. I ran three files through Crux Percolator, and then I used the resulting make-pin.pin file as input to the stand-alone version. Both report the same number of input PSMs (129,212), but the Crux version only yields a total of 26,342 PSMs, whereas the stand-alone version yields 129,212 PSMs.

The various files can be found here:

http://noble.gs.washington.edu/~wnoble/proj/malaria/2016histone-msms/results/bill/2016-09-03percolator-bug/

[Kaipo]

I think the version is different for the binary - I get the same results (26,342 for Crux and 129,212 for standalone using the binary pointed at by the script). But when I compile and run using the version here: http://cruxtoolkit.sourceforge.net/download/percolator-rel-3-00.tar.gz, I get results that are identical to the Crux version.

[William S Noble]

I have also verified that Percolator yields about 5-fold more PSMs using
the latest version versus the v3.0 tagged release. I've reported this
behavior to Lukas and Matthew.

On Wed, Sep 7, 2016 at 11:27 AM, Kaipo kaipot@users.sf.net wrote:

I think the version is different for the binary - I get the same results
(26,342 for Crux and 129,212 for standalone using the binary pointed at by
the script). But when I compile and run using the version here:
http://cruxtoolkit.sourceforge.net/download/percolator-rel-3-00.tar.gz, I
get results that are identical to the Crux version.

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• [issues:#429] https://sourceforge.net/p/cruxtoolkit/issues/429/
  Percolator does not report all of the PSMs*

Status: open
Milestone: Crux v2.0
Labels: High priority
Created: Sat Sep 03, 2016 04:31 PM UTC by William S Noble
Last Updated: Sat Sep 03, 2016 04:31 PM UTC
Owner: Kaipo

It appears that Crux Percolator does not report as many PSMs as the
corresponding stand-alone version. I ran three files through Crux
Percolator, and then I used the resulting make-pin.pin file as input to the
stand-alone version. Both report the same number of input PSMs (129,212),
but the Crux version only yields a total of 26,342 PSMs, whereas the
stand-alone version yields 129,212 PSMs.

The various files can be found here:

http://noble.gs.washington.edu/~wnoble/proj/malaria/
2016histone-msms/results/bill/2016-09-03percolator-bug/

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