NAME

propmapped - toolkit for processing next-gen sequencing data

DESCRIPTION

propMapped v2.0.1

Calculate the proportion of mapped reads/fragments.

Usage:

./prommapped [options] -i <file>

Required arguments:

-i <string>

An input file containing read mapping results. Both SAM or BAM formats are supported.

Optional arguments:

-o <string>

Name of output file including mapping statistics.

-f

If specified, fragments (read pairs) will be counted instead of individual reads. This option is only applicable for paired-end reads.

-p

If specified, only properly paired reads will be counted. This option is only applicable for paired-end reads.

AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.