countsga1
Read a chip-seq data file and computes the total number of tag counts
Usage
countsga [options]
[<]
<SGA
File>
Overview
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- version 1.5.5 where options are:
-
-h -
Show this help text
-
-d -
Print debug information
-
-f -
Feature specifications [name [+|-]]
-
-c -
Count Cut-off (default is 1)
-
The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA File>), and computes the total number of tag counts as well as the total sequence length. The <Feature> parameter is a name that corresponds to the second field of the SGA file. It might optionally include the strand specification (+|-). If no feature is given then all input tags are processed.