Run GPF
Run GPF
Description
Run GPF on de novo predicted peptides.
Input files
- exactly 1 GPF index file (.gpfindex)
- at least 1 GPF queries file (.fa | .faa | .fas | .fasta | .gpfqueries | .txt)
Output files
- GPF peptides (gpf-peptides.fasta)
- YAML results (gpf-results.yaml)
- CSV results (gpf-results.csv)
Context
Parameters
- Masses
-
Choices: monoisotopic (default)
- Similarity search
-
Choices: yes (default), no
- Mass tolerance
-
Default: 700 ppm
- Search introns
-
Choices: yes (default), no
- Max intron length
-
Default: 2100 nucl.
- Enzyme
-
Choices: Trypsin (default)
- Minimum amino acid chain length
-
Default: 5
Source code
run-gpf.rb, run-gpf.yaml (GitHub)