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chipcenter(1) | User Manuals | chipcenter(1) |
NAME¶
chipcenter - Feature Centering Tool for ChIP-seq data analysisSYNOPSIS¶
chipcenter [ options ] [ -f <feature name> ] -s <shift> [ < ] [ SGA file ]DESCRIPTION¶
chipcenter reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA file>), and shifts (by <shift>) ChIP-tag positions corresponding to a specific feature (<feature name>) to the estimated center-positions of DNA fragments. If no feature specification is set, the program accepts all oriented lines of the input SGA. Strandless features are ignored. If -r <new feature> is specified, the feature field is replaced with the <new feature> string.Launching chipcenter without any arguments will print the options list, along with their default values.
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.
OPTIONS¶
- -c <cut-off>
- A value can be specified as a cut-off for the input tag counts.
This parameter is optional. Its default value is 1.
- -d
- Show debug info.
- -f <feature name>
- This parameter is used to select all or a sub-set of chIP-seq input tags.
The feature name is specified in the second field of the SGA-formatted
input file.
If no feature name is given, then all features are selected.
- -h
- Show the usage message.
- -r <new feature>
- It defines a new feature name for feature replacement.
- -s <shift>
- It defines the relative shift (in bp) of observed ChIP-tags to estimated
center-positions of DNA fragments.
This parameter is mandatory.
- -z
- Set (output) strand to zero.
This parameter is optional.
SEE ALSO¶
chipcor(1), chipextract(1), chippeak(1) chippart(1) chipscore(1),July 2015 | Bioinformatics |