read.RepMask: Read RepeatMasker output

In FemeniasM/ExplorATEproject: Explore Active Transposable Elements from RNAseq data

Read RepeatMasker output

Description

Read a RepeatMasker output

Usage

read.RepMask(file)

Arguments

file	RepeatMasker output file

Details

This function loads the RepeatMasker output file and rename columns as:

scoreSW

Smith-Waterman score of the match, usually complexity adjusted. The SW scores are not always directly comparable. Sometimes the complexity adjustment has been turned off, and a variety of scoring-matrices are used.

PersubM

% substitutions in matching region compared to the consensus

PerBasDel

% of bases opposite a gap in the query sequence (deleted bp)

PerBasIns

% of bases opposite a gap in the repeat consensus (inserted bp)

namSeq

name of query sequence

SPMQuer

starting position of match in query sequence

EPMQuer

ending position of match in query sequence

NbasAfEQuer

no. of bases in query sequence past the ending position of match

st

match is with the Complement of the consensus sequence in the database

namRep

name of the matching interspersed repeat

classRep

the class of the repeat, in this case a DNA transposon fossil of the MER2 group (see below for list and references)

NbasCompRep

no. of bases in (complement of) the repeat consensus sequence prior to beginning of the match

SPMRepdb

starting position of match in database sequence (using top-strand numbering)

EPMRepdb

ending position of match in database sequence

nu

num index

HSM

higher-scoring match whose domain partly (<80%) includes the domain of this match.

FemeniasM/ExplorATEproject documentation built on Nov. 30, 2022, 5:26 p.m.