bowtie_aln: bowtie_aln

In mskilab/loosends: Classifying loose ends in gGraphs

bowtie_aln

Description

Perform unpaired (single end) realignment of reads to either a supplied sequence or reference FASTA

Usage

bowtie_aln(
  reads,
  ref.seq = NULL,
  ref.dir = NULL,
  ref.basename = NULL,
  outdir = "./",
  verbose = FALSE
)

Arguments

reads	(data.table with columns qname, seq)
ref.seq	(data.table with columns qname, seq)
ref.dir	(character) path to directory with reference fastas
ref.basename	(character) basename of reference fasta
outdir	(character) path to temporary output directory
verbose	(logical) default FALSE

Value

GRanges with alignment

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.