ncbi-hackathons / peptides-spectra-annotations-pasta Goto Github PK

A Docker image for the tools in the workflow is avialable here. The image includes all the prerequisites and dependencies.
To run the Docker image -

docker run -v pwd:pwd -w pwd -i -t stevetsa/proteomics:latest
This mounts the current working directory to the same directory structure inside the container. You will be able to access all files and folders downstream of the current working directory.
All the executibles are in /usr/bin, /usr/local/bin, MS-GF+ JAR file is /opt/MSGFPlusv2018.07.17.jar

add Percolator to take the mass spec identified output and recalculates the false discovery rate.

https://github.com/MSGFPlus/msgfplus/releases/tag/v2018.09.12

To use Percolator, we need to create decoy database and search them separately with MS-GF+.