/HFDiscrim

Hybrid features improve the analysis of data-independent acquisition proteomics

Primary LanguagePython

HFDiscrim

image

HFDiscrim effectively combines single-run and multi-run features to characterize chromatographic peaks

Docker image

docker pull meiyulab/hfdiscrim:1.0.0

Container creation and startup

Create a container (named hfdiscrim_work) based on the image meiyulab/hfdiscrim:1.0.0 and simultaneously mount the local folder /path/to/hfdiscrim to the folder /hfdiscrim (in the container) by running the following command in your terminal:

docker run -it --name hfdiscrim_work -v /path/to/hfdiscrim:/hfdiscrim meiyulab/hfdiscrim:1.0.0 /bin/bash

Please change /path/to/hfdiscrim to your own path.

HFDiscirm arguments

parameters descriptions
--db_fpath The output of pyprophet (merged.osw).
--chrom_dpath Directory of openswath output (.chrom.sqMass).
--work_dpath Directory for output files.
--seed Random seed for decoy generation (default: 123).
--map_size The size of the temporary database (default: 32).
--fdr_precursor FDR of precursor level (default: 0.01).
--n_mrg The number of candidate MRGroup (default: 3).
--nrt_width_percent Percentage of the search range in normalized retention time (default: 0.02).

Citation

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