---
name: "getCounts"
section: "1"
platform: "linux"
package: "bitseq"
version: "0.7.5+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/getCounts"
---

# getCounts(1)

generate read counts for each input file

## NAME

getCounts.py - generate read counts for each input file

## SYNOPSIS

**getCounts.py** \[*options*\] \[*\<inputFile.thetaMeans\>*\]*+*

## DESCRIPTION

-

  This program reads supplied .thetaMeans files and using either information from .prob files or Nmap option generates read counts for each input file provided.

## OPTIONS

- **-h**, **--help**

  show this help message and exit

- **-o** OUT, **--outFile**=*OUT*

  Output file

- **-v**, **--verbose**

  Verbose output

- **-p** PROBDIR, **--probDir**=*PROBDIR*

  Directory with .prob files. The program will look in here for files with same name except fot extension .prob in order to find out total-aligned-read counts for each experiment.

- **-n** NMAP, **--Nmap**=*NMAP*

  Comma separated list of total aligned-read-counts for each experiment.