sam2bed: Convert a SAM Format File to a BED File
In Rsubread: Mapping, quantification and variant analysis of sequencing data

Description Usage Arguments Details Value Author(s)

This function performs SAM to BED conversion. Each read in the SAM input is converted into an interval in the BED file.

sam2bed(

    samfile,
    bedfile,
    readlen)

`samfile`	a character string giving the name of input file. Input format should be in SAM format.
`bedfile`	a character string giving the name of output file. Output file is in BED format.
`readlen`	a numeric value giving the length of reads included in the input file.

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. This function does not find the read length from the SAM file, but requires the user to specify the read length.

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.

Wei Shi

Rsubread documentation built on March 17, 2021, 6:01 p.m.