getTransChromFusions: Detect trans-chromosomal mappings of Iso-seq reads

In daewoooo/primatR: What the Package Does (TODO)

Detect trans-chromosomal mappings of Iso-seq reads

Description

This function reads BAM file into a GRanges object and searches for reads that map do different chromosomal locations. Links supported by user defined number of reads are reported and points to a putative gene fusions.

Usage

getTransChromFusions(
  bamfile = NULL,
  min.mapq = 10,
  standardChroms = TRUE,
  min.links = 5
)

Arguments

bamfile	Bamfile with aligned reads.
min.mapq	Minimum mapping quality when importing from BAM files.
standardChroms	If set to TRUE only standard chromosomes (1-22, X & Y) will be kept.
min.links	Minimum number of supporting Iso-seq reads in order to report a putative gene fusion.

Value

A GRanges object reporting all found links.

Author(s)

David Porubsky

daewoooo/primatR documentation built on March 28, 2024, 6:41 a.m.