Skip to content

Improve readability of usage.md documentation #16

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
kamurani wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Improve readability of usage.md documentation #16

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
2f3c8be
readability
kamurani Jun 28, 2023
affc469
fix newline
kamurani Jun 28, 2023
264cbc7
change to backticks
kamurani Jun 28, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 10 additions & 2 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,15 @@ Alternative to the above --mzml this would pass a mzML definition (txt) file whi

The file itself is tab-separated without header, contains a single line per mzML file specified as follows:
`/path/to/file instrument_type sample_or_sampleset_name OPTIONAL:fractionation_plate_name OPTIONAL:fraction_nr`
Fractionation is automatically detected from this file, and enforced if ANY of the files have a fraction. This mainly has implications for QC though, identification and quantification are not much impacted by specifying fractionation. Instrument type can currently be one of 'qe', 'qehf', 'velos', 'lumos', 'qehfx', 'timstof', or 'lowres'.
Fractionation is automatically detected from this file, and enforced if ANY of the files have a fraction. This mainly has implications for QC though, identification and quantification are not much impacted by specifying fractionation. Instrument type can currently be one of
* `qe1`
* `qehf`
* `velos`
* `lumos`
* `qehfx`
* `timstof`
* `lowres`

Examples of instruments can be found in [this MSGF+ parameter file](https://github.com/MSGFPlus/msgfplus/blob/master/docs/ParameterFiles/MSGFPlus_Tryp_NoMods_20ppmParTol.txt).

### Input sequences: `--tdb`
Expand All @@ -142,7 +150,7 @@ peptides, specify `--phospho` to inform the search engine about this.


### Output types
The pipeline will produce by default PSM, peptide, and protein tables. You may pass FASTA databases that contain mixtures of ENSEMBL, Uniprot, or other types of entries. Use `--genes` and `--ensg` to output a gene(name)-centric table and an ENSG-centric table. If you rather have less output, use `--onlypeptides` to not output a protein table. If you have a HiRIEF table of predicted isoelectric points for peptides, you
The pipeline will produce by default PSM, peptide, and protein tables. You may pass FASTA databases that contain mixtures of ENSEMBL, Uniprot, or other types of entries. Use `--genes` and `--ensg` to output a gene(name)-centric table and an ENSG-centric table. If you would rather have less output, use `--onlypeptides` to not output a protein table. If you have a HiRIEF table of predicted isoelectric points for peptides, you
may specify it by `--hirief /path/to/table.txt`.


Expand Down