sam2bed: Convert a SAM format file to a BED format file
Description
SAM to BED conversion
Usage
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.
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.
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.