rbh: Find Reciprocal Best Hits using Blat

In gschofl/genoslideR: Create and manipulate multiple genome alignments with annotation.

Description

Find Reciprocal Best Hits using Blat

Usage

rbh(seq_files, anno_files = NULL, anno_type = "glimmer3",
  blatopts = list(), glimmeropts = list(o = 50, g = 110, t = 30),
  wd = NULL)

Arguments

seq_files	Path to sequence files ('fasta' or 'genbank').
anno_files	(Optional) Path to annotation files. If no annotation files are provided an ab initio annotation using glimmer3 is performed.
anno_type	Type of annotation ('glimmer3', 'genbank', 'gff', 'ptt', or 'ftable').
blatopts	Options passed to blat.
glimmeropts	Options passed to glimmer3 if an ab initio annotation is performed.
wd	Working directory. Defaults to the parent directory of the provided sequence files.

Details

rbh will create a hidden directory ‘.rbh’ in the parent directory of the submitted sequence files and place all results of the intermediate computational steps in this directory.

The results of a rbh run are stored in a directory ‘rbh’ in the parent directory of the submitted sequence files.

gschofl/genoslideR documentation built on May 17, 2019, 8:52 a.m.