denisbeslic/denovopipeline

Pipeline for de novo peptide sequencing (Novor, DeepNovo, SMSNet, PointNovo, Casanovo) and assembly with ALPS.

denovopipeline's Issues

pNovo and search parameters

Hey Denis,

Thank you very much for providing the pipeline! I have couple of *.mgffiles and trying to run the different de-novo algorithms of them. Regarding the de-novo algorithms, I have couple of questions:

• How did you use pNovo? I installed it from the pfind website and the installation worked as usual, after opening the tool (pNovo3_Search.exe) I tried to run small toy example, I exactly did the same steps as in the user guide from pFind by choosing the input file and selecting the output dir path (all parameters are kept as default), after couple of seconds the progress output window shown that the process is completed but the search button still loading for couple of hours without writing any results (only empty results files e.g. result.res….etc.). I tested the tool with DeNovoGUI and everything worked very well and fast, but the output file is only the pNovo.res, which contains all searching result. Your pipeline is expecting the file result.res, which records the top-one PSM per spectrum. Is there any way to filter out the pNovo.res or to use it in your pipeline?
• As I am using different files, there are different search parameters/modifications. By running Novor, Casanovo and pNovo3(using DeNovoGUI), I had no problem with selecting these parameters. Is there any way to set parameters in SMSNet and DeepNovo? In PointNovo should I just change the parameters in resources/PointNovo/config.py?

Best,

How to process specific enzymes

When I want to process files with other enzymes than trypsin, Should I change the parameters manually?

Use psm_utils to access peptideshamer summary file

Add Casanovo

Make summary script work only with subset of tools

Refactor assembly script