sam2bed {Rsubread} | R Documentation |
SAM to BED conversion
sam2bed(samfile,bedfile,readlen)
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. |
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.
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