get_valid_hybrids: Get valid hybrids

In amchakra/toscatools: Tosca proximity ligation pipeline toolkit

Get valid hybrids

Description

Calculate valid hybrids from Blat partial alignments

Usage

get_valid_hybrids(
  blast.query.dt,
  min_unmapped_length = 16,
  q_minoverlap = 4,
  q_maxgap = 4,
  s_minoverlap = 0,
  xlink_distance = 5,
  max_read_length = 100
)

Arguments

min_unmapped_length	Minimum unmapped read length
q_minoverlap	Maximum overlap in left and right query arms
q_maxgap	Maximum gap between left and right query arms
s_minoverlap	Minimum overlap in left and right subject arms
xlink_distance	Maximum distance from start of the read (i.e. crosslink + 1 nt) before left arm starts
blast8.query.dt	blast8 data.table with read length and metrics

Value

Hybrids data.table

amchakra/toscatools documentation built on Nov. 26, 2022, 12:35 p.m.