sam2bed: Convert a SAM format file to a BED format file

Description Usage Arguments Details Value Author(s)

View source: R/sam2bed.R

Description

SAM to BED conversion

Usage

1
sam2bed(samfile,bedfile,readlen)

Arguments

samfile

character string giving the name of input file. Input format should be in SAM format.

bedfile

character string giving the name of output file. Output file is in BED format.

readlen

numeric value giving the length of reads included in the input file.

Details

This function converts a SAM format file to a BED format file, which can then be displayed in a genome browser like UCSC genome browser, IGB, IGV.

Value

No value is produced but a BED format file is written to the current working directory. This file contains six columns including chromosomal name, start position, end position, name(‘.’), mapping quality score and strandness.

Author(s)

Wei Shi


Rsubread documentation built on Nov. 9, 2018, 6 p.m.