From ea6a39e3f84059f51c7ecfe355990165565a9ef2 Mon Sep 17 00:00:00 2001 From: Kendell Clement Date: Tue, 7 Nov 2023 16:31:06 -0700 Subject: [PATCH] Include parameter --assign_ambiguous_alignments_to_first_reference in readme --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index efd3ceeb..571a121d 100644 --- a/README.md +++ b/README.md @@ -267,6 +267,8 @@ This should produce a folder called 'CRISPResso_on_base_editor'. Open the file c --expand_ambiguous_alignments: If more than one reference amplicon is given, reads that align to multiple reference amplicons will count equally toward each amplicon. Default behavior is to exclude ambiguous alignments. (default: False) +--assign_ambiguous_alignments_to_first_reference: If more than one reference amplicon is given, ambiguous reads that align with the same score to multiple amplicons will be assigned to the first amplicon. Default behavior is to exclude ambiguous alignments. (default: False) + --needleman_wunsch_gap_open: Gap open option for Needleman-Wunsch alignment (default: -20) --needleman_wunsch_gap_extend: Gap extend option for Needleman-Wunsch alignment (default: -2)