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    (JR) Ray Sajulga
    @jraysajulga
    Hello! I am interested in importing PepQuery into Galaxy. Just wondering how licensing works with PepQuery.
    lthp
    @lthp
    Hi, I have noticed some issues that prevent from running pepQuery properly: http://www.pepquery.org/data/msdatasets.tar.gz and http://www.pepquery.org/data/msdatasets.json are not accessible to the public. Besides, the dataset http://www.pepquery.org/data/iPRG2015.tar.gz does not include the shell script mentioned.
    courcelm
    @courcelm
    Hello, the following link is broken: http://www.pepquery.org/data/PepQuery_v1.0.0.tar.gz , is there a way to get this file to obtain the test data and script?
    courcelm
    @courcelm
    Is it possible to set the min and max peptide mass?
    Bo
    @wenbostar
    @courcelm , we don't have parameters to control the peptide mass but you could use "-minLength" and "-maxLength" to limit the peptides considered in the search.

    Hello, the following link is broken: http://www.pepquery.org/data/PepQuery_v1.0.0.tar.gz , is there a way to get this file to obtain the test data and script?

    @courcelm , you could find example data at http://pepquery.org/data/iPRG2015.tar.gz.

    md.qudratullah
    @qudratbt_twitter
    Hello, I have run PepQuery but in psm_rank.txt file the column "confident" is missing
    Bo
    @wenbostar
    @qudratbt_twitter , sorry for the late reply. I didn't check gitter frequently. If the column "confident" is missing in psm_rank.txt, it means all the PSMs in the file are not confident based on p-value or competitive filtering based on unrestricted post-translational modification searching.