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snijderlab / stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
MIT License
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confused result #247

Closed biocc closed 6 months ago

biocc commented 6 months ago

Dear sir, well done in the stitch 1.5, with satisfied speed. But in the assembled sequence, there are some J-amino acids. I don't understand the result. Can you help me?

douweschulte commented 6 months ago

J is the amino acid code for I or L. It is used in Stitch to indicate that peptides have no support specifically for I or L. You can see this at the very bottom of the details page of all peptides. Do keep in mind that this is only done for XleDisambiguation in any other case the I/L are taken at face value and used as such.

douweschulte commented 6 months ago

Here is the full definition ambiguous/unusual amino acids