---
name: "propmapped"
section: "1"
platform: "linux"
package: "subread"
version: "2.0.8+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/propmapped"
---

# propmapped(1)

toolkit for processing next-gen sequencing data

## NAME

propmapped - toolkit for processing next-gen sequencing data

## DESCRIPTION

propMapped v2.0.4

-

  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 Alexandre Mestiashvili for the Debian distribution and\
  can be used for any other usage of the program.