Annotating Contaminants in FASTA Files

[rolivella]

Hi,

I'm looking for information on how Philosopher annotates contaminants in FASTA files. I checked the documentation here, but couldn't find the details I need. The command I'm using is:

philosopher database --custom $fastafile --contam

Any help would be appreciated.

Thanks!

[fcyu]

It works only when you download the fasta file using Philosopher. Using your own fasta file won't append anything to the contaminant proteins.

Best,

Fengchao

[rolivella]

Thanks @fcyu , so the option --contam in this case does nothing? Can I skip it?

[fcyu]

It adds the contaminant proteins to your fasta file, but won't append the contam_ prefix if I remember it correctly.

Best,

Fengchao