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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").

Example of the SmoothedReads track in the Genome Browser
Example of the SmoothedReads track in the Genome Browser
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