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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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How to set semi-specific digestion to the FASTA file with DIANN #1156

Open crf2213 opened 2 months ago

crf2213 commented 2 months ago

There are two warnings when I processed my data with DIANN, I set "--semi" in the command window,however it seems doesn't work. The following warnings or errors (in alphabetic order) were detected at least the indicated number of times: WARNING: --semi will have no effect when digesting a FASTA, disabled : 1 WARNING: it is strongly recommended to first generate an in silico-predicted library in a separate pipeline step and then use it to process the raw data, now without activating FASTA digest : 1

vdemichev commented 2 months ago

Hi,

Yes, please just follow the suggestions DIA-NN prints in these warnings. The --semi option is meant to be used in combination with 'Reannotate' https://github.com/vdemichev/DiaNN?tab=readme-ov-file#command-line-reference.

Best, Vadim