Elementolab/ChIPseeqerDensityMatrix
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| ChIPseeqerDensityMatrix --targets='''TF_targets.txt''' --chipdir='''CHIP''' | ChIPseeqerDensityMatrix --targets='''TF_targets.txt''' --chipdir='''CHIP''' | ||
| + | |||
| + | For example: | ||
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| + | ChIPseeqerDensityMatrix --genome=mm9 --chipdir=CHIP/ --generegion=TSS --db=refSeq --format=sam --targets=peaks.txt | ||
| The following options are available: | The following options are available: | ||
| - | --targets=FILE file containing genomic regions | + | --targets=FILE file containing genomic regions (or "all" but only in latest svn version) |
| --chipdir=DIR folder containing the reads | --chipdir=DIR folder containing the reads | ||
| --norm=INT set to 1 to normalize the matrix | --norm=INT set to 1 to normalize the matrix | ||
Revision as of 18:40, 21 June 2012
Back to Elementolab/ChIPseeqer_Tutorial
ChIPseeqerDensityMatrix
In this analysis you can estimate the average read density profiles:
- for the regions around the TSS or the TES of the genes, OR
- for the regions around the summit of the peaks.
To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.
1. Type the command:
ChIPseeqerDensityMatrix --targets=TF_targets.txt --chipdir=CHIP
For example:
ChIPseeqerDensityMatrix --genome=mm9 --chipdir=CHIP/ --generegion=TSS --db=refSeq --format=sam --targets=peaks.txt
The following options are available:
--targets=FILE file containing genomic regions (or "all" but only in latest svn version) --chipdir=DIR folder containing the reads --norm=INT set to 1 to normalize the matrix --prefix=STR prefix for output files --format=STR the format of the reads (e.g., eland, bed) --fraglen=INT 0 = no read extension otherwise extend to specified value --uniquereads=INT 0/1 if 1 collapose clonal reads; 1 = recommended for TF and histone modification, not for nucleosome positioning --ws=INT the window size, can be 10, 100 etc. Default is 10. --outepsmap=FILE the name of the output eps file with the 2D density plot --xlabel=STR the label for the x axis of the 2D plot --ylabel=STR the label for the y axis of the 2D plot
- To estimate the read density profiles for the regions around the TSS or the TES of the genes, use the following options:
--generegion=STR can be TSS (transcription start site) or TES (transcription end site)
--lenu=INT length upstream of genomic region (TSS or TES). Default is 2000bp.
--lend=INT length downstream of genomic region (TSS or TES). Default is 2000bp.
--genome=STR can be hg18 (human),
mm9 (mouse),
dm3 (drosophila), or
sacser (for Saccharomyces cerevisiae)
--db=STR can be refSeq (available for hg18, mm9, dm3),
AceView (for hg18, mm9),
Ensembl (for hg18, mm9, dm3)
UCSCGenes (for hg18, mm9).
Default is refSeq.
- To estimate the read density profiles for the regions around the summit of the peaks, use the following options:
--w=INT the window size around the peak summit. Default is 2000bp.
This analysis was also described here.
IMPORTANT: Note that in the --targets option you must enter the ChIPseeqer output file.
The output of this process is a .density file. Each line corresponds to a RefSeq transcript (when --generegion=TSS or TES). For each 10 nucleotides in the region 2000b upstream to 2000b downstream, the average number of reads is computed. Thus, the .density file will look like this:
NM_007125 3.8 4.0 4.0 3.8 3.0 3.0 2.6 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 NM_004202 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.6 1.0 1.0 1.0 1.0 1.0 NM_001005852 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 2.6 1.0 NM_001146706 4.0 4.0 4.0 4.0 4.0 3.8 3.0 3.0 3.0 3.0 3.0 4.0 4.0 4.0 4.0 2.0 2.0
The number of columns per line will be (lend+lenu)/10 + 1
