proBAMconvert is a conversion tool to convert common peptide identification files (mzIdentML, pepXML, mzTAB) to the proBAM or proBED format, as defined by the HUPO Proteomics Standards Initiative. In essence, proBAMconvert reads peptide identification files, maps identified peptides onto the genome and writes output into the proBAM/proBED format.
For more information about how proBAMconvert works you can consult the manual,
where proBAMconvert is explained step by step alongside a tutorial. Click here to open the manual.
We are constantly looking for ways to improve proBAMconvert, if you encounter any issues or have some suggestions don't hesitate to post on our
github issue page.
Thanks to Björn Grüning and Jim Johnson we now have a bioconda package and galaxy implementation of proBAMconvert in testing phase.
link to galaxy test toolshed
proBAMconvert is also available on our galaxy server
link to proBAMconvert bioconda package