checkPEReads: Check if both mates of a read pair are consistent with the...

In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data

Description

This function tests if the two fragments of a chimeric read fall within the range defined defined by the backsplice junctions. Using the genome coordinates of the acceptor and donor (columns 2 and 5 in Chimeric.out.junction), the function checks if the region covered by the two fragments of the chimeric reads (i.e. column 11 plus the width of the CIGAR string in column 12 and column 13 plus the width of the CIGAR string in column 14) are within the region spanned by the acceptor and donor sites. By setting the end tollerance (endTol) you can allow for some coverage outside the circularized region.

Usage

checkPEReads(df, endTol = 5)

Arguments

df	Chimeric.out.junction table returned by getCandidateBackspliceSites
endTol	How many nucleotides on the "wrong" side of the junction can be tolerated.

Value

Logical vector

KasperThystrup/circulaR documentation built on March 14, 2021, 12:44 p.m.