getCandidateBackspliceSites: Read candidate backsplice sites from Chimeric.out.junction...

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

Description

getCandidateBackspliceSites reads entire Chimeric.out.junction file and returns reads consistent with backsplicing. Candidate backsplice junctions are identified by applying the following filters

1. Donor and acceptor are on the same chromosome

2. Donor and acceptor are on the same strand

3. The acceptor is upstream of donor (On plus strand: acceptor position < donor position ; On minus strand: donor position < acceptor position)

4. Distance between donor and acceptor is no more than 100.000 bases (by default, can be changed)

Usage

getCandidateBackspliceSites(
  fn,
  backSpliceDist = 1e+05,
  seqAcrossSj = TRUE,
  libType = "fr-firststrand",
  verbose = FALSE
)

Arguments

fn	Path to a Chimeric.out.junction file.
backSpliceDist	The maximum allowed distance between donor and acceptor sites.
seqAcrossSj	Boolean indicating whether to return all backspliced reads or just reads where one of the mates span the candidate backsplice site.
libType	Character string indicating which stranded library protocol was used to generate the data, must be 'fr-firststrand' for e.g. dUTP method or 'fr-secondstrand'.
verbose	Inlcude basic statstics on the chimeric readsm ust be logical (default FALSE).

Value

tibble of reads covering backsplice sites

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