filter_counts1
Read a chip-seq data file and filters out all read counts
Usage
filter_counts [options]
[<]
<SGA
File>
Overview
-
- version 1.5.5 where options are:
-
-h -
Show this help text
-
-d -
Print debug information
-
-f -
Feature defining the user-defined regions of interest (default=RMSK)
-
-r -
Retain Mode on
-
The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA File>) and filters out all read counts that occur within user-defined regions of interest, such as Repeat Mask regions (feature=RMSK). If 'Retain Mode' is on, it only retains those lines that are within the user-defined regions, in which case the annotation of the user-defined regions is added to the output SGA file.