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KarchinLab / bigmhc

BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
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bits files in makeseqs #9

Closed cmf1997 closed 6 months ago

cmf1997 commented 7 months ago

hello there: wonderful work for predicting affinity of peptide and mhc, I am trying to generate pseudo sequences following the jupyter, in the instruction I do not see how bits file was generating? it would be much appreciated if you can provide any suggestions! thank you !

benjaminalbert commented 6 months ago

Hi, @cmf1997, I apologize for the delay. We have added step-by-step instructions for generating pseudosequences to the makeseqs.ipynb notebook. Please let me know if this answers your question!

cmf1997 commented 6 months ago

thanks for you reply! I have tried the make logo function in sam tool, but It only return a eps file ./makelogo mhc -i mhc.mod &> mhc.bits I assumed this code would return a bits file, but actually did not, also, I generate bits from eps file, but it's such a dummy solution, this there anything I missed?

benjaminalbert commented 6 months ago

Did you build from the source provided? The source has been modified to print out the entropy. I will make a note of this in the notebook to clarify.

cmf1997 commented 6 months ago

that must be something I miss, I check the README, there is a Installation step ./sam-t-configurewhich perl`, I will run it again! it would be much easier to reproduce if you can clarify. thanks a lot!

benjaminalbert commented 6 months ago

The SAM README is potentially outdated. Although we provided all the SAM source code along with its original instructions, following the instructions specifically in the makeseqs.ipynb notebook are all you should need. Let me know if that resolves things for you!

cmf1997 commented 6 months ago

thanks for your explicitly reply! I would check for it once available