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Repository bigwig_outlier_bed

Name: bigwig_outlier_bed

Owner: iuc

Synopsis: pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files

Detailed description:

Bigwigs are great. Peaks are easy to see. Small runs of very low values not so much

Using numpy to segment bigwig values into regions of contiguous high and low values, this tool writes bed files
containing those regions, with a score set to 1 or -1 depending on whether above the top quantile or below the
low quantile.

Quantile values recommended are 0.01 and 0.99. They are calculated for each chromosome and vary a bit.
Ideally should be estimated over the entire assembly but not feasible without sampling due to RAM hoggery.
Minimum window size of 10 will give a very, very low risk of random false positives at about 0.01**10 for 0.01
quantile cutoff for example.

Content homepage: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/bigwig_outlier_bed/ebcd48f183b3

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bigwig_outlier_bed

Type: unrestricted

Revision: 0:ebcd48f183b3

This revision can be installed: True

Times cloned / installed: 73

Contents of this repository

Name	Description	Version	Minimum Galaxy Version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Bigwig extremes to bed features View tool metadata	Writes high and low bigwig runs as features in a bed file	0.1.4	22.05