Questions about the generic input format about flashlfq HOT 3 CLOSED

Hi Will. We'll get you answers soon.

from flashlfq.

1. Short answer: including or excluding the path and/or extension is OK.

Long answer: FlashLFQ will trim the spectra files you pass down to the filename (without path or extension) and will do the same to the filename column in the PSMs file. If the PSM's spectra file without extension is not present in the list of spectra files without extensions, then the PSM is skipped. So including a full path or extension is OK; both of these will get stripped out. However the program will probably get messed up if you include an extra period in the spectra name, because FlashLFQ will think this is part of the extension.

2. This is not well documented, but for generic PSM files the delimiter is the semicolon character (";"). Currently there is no way to use a custom character to delimit proteins. I'll fix the generic example file, because as you pointed out, it uses the | character. We use this character in MetaMorpheus to delimit proteins within a protein group, and we treat this as a different scenario than delimiting protein groups from each other.

Thanks for integrating FlashLFQ into mokapot, I'm excited to see how it goes! We're always happy to provide support.

from flashlfq.

Great - thank you for the details!

from flashlfq.