Commit b4688da4 authored by Moustakas's avatar Moustakas
Browse files

Improve phrasing

parent 4ee4ee23
# WipeReads
## Introduction
WipeReads is a tool for removing reads from indexed BAM files.
It respects pairing information and can be set to remove reads whose duplicate
maps outside of the target region. The main use case is to remove reads mapping
to known ribosomal RNA regions (using a supplied BED file containing intervals for these regions).
WipeReads is a tool for removing reads from indexed BAM files that are inside a user defined region.
It takes pairing information into account and can be set to remove reads if one of the pairs maps outside of the target region.
An application example is to remove reads mapping to known ribosomal RNA regions (using a supplied BED file containing intervals for these regions).
## Example
To open the help menu:
......@@ -62,5 +61,5 @@ biopet tool WipeReads --input_file myBam.bam \
~~~
## Output
This tool outputs a bam file containing all the reads not inside a ribosomal region.
And optionally a bam file with only the ribosomal reads
This tool outputs a bam file containing all the reads not inside the ribosomal region.
It can optionally output a bam file with only the reads inside the ribosomal region
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