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This analysis create a read density track for the UCSC Genome Browser.
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:
ChIPseeqerMakeReadDensityTrack --readdir=CHIP/ --format=sam --trackname="Read density"
The following options are available:
--readdir=DIR Define the directory that contains the ChIP reads (one file per chromosome, reads.chr1 etc). --format=STR Define format of the read files: bam, sam, eland, exteland, export, bed. Default is eland. --trackname=DIR Define the name of the peaks track. --outfile=STR Define the name of the output file. --uniquereads=INT When set to 1, removes clonal reads (i.e., when several identical reads map to the same exact position in the genome). Default is 1. --normalize=INT When set to 1, normalization of read density id performed. Default is 1. --chrdata=STR To run for different organisms, point to files: DATA/hg19.chrdata for human hg19 DATA/hg18.chrdata for human hg18 DATA/mm10.chrdata for mouse mm10 DATA/mm9.chrdata for mouse mm9 DATA/rn4.chrdata for rat rn4 DATA/dm3.chrdata for drosophila DATA/sacser.chrdata for Saccharomyces cerevisiae --ws=INT Define window size for smoothing. Default is 10bp.
This command will create a gzipped file name Read_density.wig.gz.
You can then point your Web browser to UCSC Genome Browser, and upload the track in the "Add custom tracks" section (or "Manage custom tracks").