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Examples of how to use CREAD tools

Many examples can be found in the man pages. This page will be updated with additional examples.

bed-site examples

The bed-site program converts the output for storm and modstorm to bed and html files for creating webpages with links to tracks on the UCSC browser.

Example files

This File may be used to try the examples below

storm.out modstorm.out

Example 1

bed-site -b example.bed -o index.shtml -p user/example \
-t hostmachine -g mouse -d mm5 storm.out

This takes the output from storm in storm.out , and produces index.shtml and example.bed . When these two files are placed on a web-server on hostmachine at the path /user/example, they create a webpage detailing the module sites with a link to a track on the UCSC browser.

Example 2

bed-site -M -b example.bed -o index.shtml -p user/example \
-t hostmachine -g human -d hg18 modstorm.out

This takes the output from modstorm in modstorm.out , and produces index.shtml and example.bed . When these two files are placed on a web-server on hostmachine at the path /user/example, they create a webpage detailing the module sites with a link to a track on the UCSC browser.