cannot get same peptide in result

Tseng722 commented 12 months ago

Installation Type

Standalone

pVACtools Version / Docker Image

4.0.2

Python Version

3.9.18

Operating System

No response

Describe the bug

my input peptide cannot match the result in .all_epitopes.aggregated.tsv input peptide

CTDDNALAYY
TVSDYISELY
AVSDVCNSLY
SSDDLNYIYY
ATDALMTGYT
output peptide
CTDDNALAY
VSDYISELY
VSDVCNSLY
SSDDLNYIY
ATDALMTGY

the missing amino acid always happens at first or end position. i thought i use this command,-e1 8,9,10,11,12, might get at least the same peptide as original.

How to reproduce this bug

pvacbind run  \
/path/test.fasta  \
test  \
HLA-A*01:03  \
NetMHCpan NetMHC  \
/path/test \
-e1 8,9,10,11,12   \
-k  \
-t 48  \
-b 100000 \       <- i don't want any peptide filtered when run net-chop
--aggregate-inclusion-binding-threshold 100000 \         <- i don't want any peptide filtered when run net-chop
--net-chop-method cterm  \
--netmhc-stab   \
--iedb-install-directory /CMU_TSA/joyce7625e5/TSA_tool/data/iedb/

Input files

No response

Log output

na

Output files

No response

susannasiebert commented 12 months ago

The aggregate report picks the best epitope among all the predicted epitopes for each peptide sequence in your input fasta. In your case, with the parameter -e1 8,9,10,11,12, it evaluates all of the 8mers, 9mers, and 10mers derived from the original input peptides (the input peptides are too short for 11mers and 12mers) and picks the best one among them, i.e. the one with the lowest IC50 binding affinity. You can see the full list of results for all epitopes in the test.all_epitopes.tsv file. If you only want to evaluate the exact peptides in your input fasta without any of the shorter epitopes, you can set -e1 10.

Please also see our documentation for more details.

susannasiebert commented 10 months ago

Closing this issue due to inactivity.

griffithlab / pVACtools