diff --git a/docs/tools/WipeReads.md b/docs/tools/WipeReads.md index 0263e1b7fa14c8f6884a8e6f601025137cad4e29..6c26fe2eed5757a1969c80899e61244e9a7967d2 100644 --- a/docs/tools/WipeReads.md +++ b/docs/tools/WipeReads.md @@ -1,10 +1,9 @@ # 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