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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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Annotate zero confidence positions in structural reads #211

Closed douweschulte closed 1 year ago

douweschulte commented 1 year ago

Just exchange the sequence with X when the confidence is 0.

douweschulte commented 1 year ago

Not sure what this would add, when the score is zero it is not taken anyway for any consensus alignment. The only help would be in sequence alignment, Xs are placed anywhere while the original AA could shift the alignment into a worse one.