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cschlaffner / PoGo

PoGo is a proteogenomic tool which allows mapping of peptides identified through mass spectrometry to a reference genome through provided gene annotation.
http://www.sanger.ac.uk/science/tools/pogo
GNU General Public License v3.0
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Pogo Issue in Human wrong mapping to chromosome 2b #11

Closed ypriverol closed 7 years ago

ypriverol commented 7 years ago

@cschlaffner We have a problem with the current version of the pogo. I just added the following file with the current version of pride cluster peptides. When the mapping finish some of the peptides are the map to chromosome 2b, What is the reason of that if this chromosome is not in my input. The ENSEMBL browser does not check for that but if I add the chr option to the bed and load into UCSC it will complain.

Here the input. pride_cluster_peptides_9606_Human.pogo.zip

cschlaffner commented 7 years ago

This issue has been resolved with the latest commit.

ypriverol commented 7 years ago

Hi @cschlaffer thanks for fixing the error. I have added the chr option to the tool. Do you know if the bed files based on ensembl fasta/gtf files is ucsc now compliant? Are the differences with the 0 or 1 based standard affecting us?