is_hdr_strict: Figure out which reads conform to the HDR using the donor.

In valenlab/amplican: Automated analysis of CRISPR experiments

Figure out which reads conform to the HDR using the donor.

Description

This is strict detection as compared to 'is_hdr' which was designed to be less specific and allow for all kinds of donors. This method requires that you have exactly the same events (mismatches, insertions, deletions) as the difference between amplicon and donor sequences. It ignores everything else, so other mismatches and small indels etc. as noise are allowed here for valid HDR.

Usage

is_hdr_strict(aln, cfgT, scoring_matrix, gap_opening = 25, gap_extension = 0)

Arguments

aln	(data.table) This are events that contain already consensus column, they are also shifted and normalized.
cfgT	(data.table) Config data.table with columns for amplicon and donor.
scoring_matrix	(scoring matrix)
gap_opening	(integer)
gap_extension	(integer)

Value

(aln) same as aln on entry, but readType is updated to TRUE when read is recognized as HDR

valenlab/amplican documentation built on Jan. 28, 2024, 5:10 a.m.