Mercurial > repos > iuc > bigwig_outlier_bed
diff README.md @ 0:ebcd48f183b3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
| author | iuc |
|---|---|
| date | Fri, 05 Jul 2024 06:00:15 +0000 |
| parents | |
| children | 61946b8bd43b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Jul 05 06:00:15 2024 +0000 @@ -0,0 +1,31 @@ +## bigwig peak bed maker + +### July 30 2024 for the VGP + +This code will soon become a Galaxy tool, for building some of the [NIH MARBL T2T assembly polishing](https://github.com/marbl/training) tools as Galaxy workflows. + +JBrowse2 2.12.3 update will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below. + +### Find and mark BigWig peaks to a bed file for display + +In the spirit of DeepTools, but finding contiguous regions where the bigwig value is either above or below a given centile. +0.99 and 0.01 for example. These quantile cut point values are found and applied over each chromosome using some [cunning numpy code](http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html) + + + + + +Big differences between chromosomes 14,15,21,22 and Y in this "all contigs" view - explanations welcomed: + + + + +[pybedtools](https://github.com/jackh726/bigtools) is used for the bigwig interface. Optionally allow +multiple bigwigs to be processed into a single bed - the bed features have the bigwig name in the label for viewing. + +### Note on quantiles per chromosome rather than quantiles for the whole bigwig + +It is just not feasible to hold all contigs in the entire decoded bigwig in RAM to estimate quantiles. It may be +better to sample across all chromosomes so as not to lose any systematic differences between them - the current method will hide those +differences unfortunately. Sampling might be possible. Looking at the actual quantile values across a couple of test bigwigs suggests that +there is not much variation between chromosomes but there's now a tabular report to check them for each input bigwig.