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RnaChipIntegrator is a utility that performs integrated analyses of RNA-Seq and ChIP-Seq data, identifying the nearest ChIP peaks to each transcript, and vice versa. The individual analyses differ from each other according to the criteria that are used to calculate the distances between peaks and transcripts.
The program was originally written specifically for ChIP-Seq and RNA-Seq data but can be used with any set of genomic features e.g. canonical genes, CpG islands etc, or expression data e.g. microarrays.
The most basic form of usage is:
RnaChipIntegrator <rna-data-file> <chip-data-file>
The RNA-seq data file must be a tab-delimited file with 5 columns of data for each genomic feature (one per line):
# ID chr start end strand
chr is the chromosome name, start and end define the limits of the feature,
and strand must be either + or -. ID is a name which is used to identify the
genomic feature in the output.
Optionally there can be a 6th column, indicating whether the gene was differentially expressed (= 1) or not (= 0).
The ChIP-seq data file must be a tab-delimited file with 3 columns of data for each ChIP peak (one per line):
# chr start end
chr is the chromosome name (must match those in the RNA-seq file), and start
and end define the ChIP peaks - these can either be summits (in which case
'end' - 'start' = 1), or regions (with 'start' and 'end' indicating the extent).
Note that different analyses will be selected depending on whether the ChIP peaks are defined as summits or regions.
See the Manual page for more detail on the program's operation and the analyses that are run.
Also running
RnaChipIntegrator.py -h
will produce a list of options and descriptions of their functions.
The output of the program consists of one tab-delimited file for each analysis that was performed, plus an XLS spreadsheet which has all the results plus a "notes" page that explains the data from each analysis.
For full descriptions of each analysis see the README document in the doc
subdirectory.
See Download and Install.
Example data files can be found in the examples subdirectory, and which can be used
as input to the program for test or demonstration purposes; see the README file in
the same directory for more information.
This software is licensed under the Artistic License 2.0; see the LICENSE document.
See the [Manual](https://github.com/fls-bioinformatics-core/RnaChipIntegrator/wiki/RnaChipIntegrator: Manual) page for more detailed descriptions of each analysis, the available options, and the outputs from the program.