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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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how pvacseq select netchop result #738

Closed asmlgkj closed 2 years ago

asmlgkj commented 2 years ago

Thanks a lot for developing such a powerful tool. I am a little confused when pvacseq used netchop to predict the netchop score.

for example, a fasta sequnece


$cat test.txt1

>KAVYNFATC FQPQNGQFI
command
netchop test.txt1 > test.myout12
result is NetChop 3.0 predictions using version C-term. Threshold 0.500000

pos AA C score Ident

1 F S 0.678299 KAVYNFATC 2 Q . 0.023621 KAVYNFATC 3 P . 0.066250 KAVYNFATC 4 Q . 0.078159 KAVYNFATC 5 N . 0.034841 KAVYNFATC 6 G . 0.040971 KAVYNFATC 7 Q . 0.264217 KAVYNFATC 8 F S 0.704804 KAVYNFATC 9 I . 0.355054 KAVYNFATC

Number of cleavage sites 2. Number of amino acids 9. Protein name KAVYNFATC
how will pvacseq give the score for this peptide?

susannasiebert commented 2 years ago

Running NetChop will output 3 additional columns in the pVACseq filtered report (documentation):

Best Cleavage Position: Position of the highest predicted cleavage score Best Cleavage Score: Highest predicted cleavage score Cleavage Sites: List of all cleavage positions and their cleavage score where the cleavage score is above the chosen threshold (--net-chop-threshold)

asmlgkj commented 2 years ago

thanks a lot