Elementolab/ChIPseeqer Species
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| Other programs in the ChIPseeqer framework that you need to specify | Other programs in the ChIPseeqer framework that you need to specify | ||
| - | * the genome (e.g., -genome "hg18") and/or | + | * the genome (e.g., --genome=hg18) or |
| + | * the database (e.g., --db=AceView) or | ||
| * the gene annotation files (e.g., annotation=DATA/mm9/refGene.txt.mm9.20APR2010) | * the gene annotation files (e.g., annotation=DATA/mm9/refGene.txt.mm9.20APR2010) | ||
| are: | are: | ||
Revision as of 20:17, 19 April 2011
SUPPORTED SPECIES
The species currenty supported in ChIPseeqer are:
- Human (acembly hg18) - Default in all ChIPseeqer programs
- Mus musculus (acembly mm9)
- Drosophila melanogaster (acembly dm3)
- Saccharomyces cerevisiae
To run ChIPseeqer on a species make sure to use the option:
-chrdata STR to run for organisms other that human (default is hg18), point to files:
DATA/mm9.chrdata for mouse,
DATA/dm3.chrdata for drosophila or
DATA/sacser.chrdata for Saccharomyces cerevisiae
Other programs in the ChIPseeqer framework that you need to specify
* the genome (e.g., --genome=hg18) or * the database (e.g., --db=AceView) or * the gene annotation files (e.g., annotation=DATA/mm9/refGene.txt.mm9.20APR2010)
are:
ChIPseeqerAnnotate ChIPseeqerSummaryPromoters ChIPseeqerFindClosestGenes ChIPseeqerFindDistalPeaks ChIPseeqerDensityMatrix ChIPseeqerPlotAverageReadDensityInGenes ChIPseeqerPlotAveragePeaksNumberInGenes ChIPseeqerCreateRandomRegions
HOW TO ADD A NEW SPECIES
1. You need to make a .chrdata file for the new organism, that will look like this:
chr10 129993255 0.840 chr11 121843856 0.866 chr12 121257530 0.797 chr13 120284312 0.816 chr14 125194864 0.781 chr15 103494974 0.842 chr16 98319150 0.838 chr17 95272651 0.812 chr18 90772031 0.837 chr19 61342430 0.830
and the columns indicate (chromosome_name chromosome_size chromosome_mappability)
To create this file follow the steps here.
2. Add the .chrdata to the ChIPseeqer/DATA/ folder
