Mercurial > repos > fubar > bigwig_outlier_bed
comparison README.md @ 0:94fe59a127a0 draft default tip
planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
| author | fubar |
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| date | Mon, 01 Jul 2024 03:31:33 +0000 |
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| 1 ## bigwig peak outlier to bed | |
| 2 | |
| 3 ### July 30 2024 for the VGP | |
| 4 | |
| 5 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. | |
| 6 | |
| 7 The next JBrowse2 tool release will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below. | |
| 8 | |
| 9 ### Find and mark BigWig peaks to a bed file for display | |
| 10 | |
| 11 In the spirit of DeepTools, but finding contiguous regions where the bigwig value is either above or below a given centile. | |
| 12 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) | |
| 13 | |
| 14  | |
| 15 | |
| 16  | |
| 17 | |
| 18 Big differences between chromosomes 14,15,21,22 and Y in this "all contigs" view - explanations welcomed: | |
| 19 | |
| 20  | |
| 21 | |
| 22 | |
| 23 [pybedtools](https://github.com/jackh726/bigtools) is used for the bigwig interface. Optionally allow | |
| 24 multiple bigwigs to be processed into a single bed - the bed features have the bigwig name in the label for viewing. | |
| 25 | |
| 26 ### Note on quantiles per chromosome rather than quantiles for the whole bigwig | |
| 27 | |
| 28 It is just not feasible to hold all contigs in the entire decoded bigwig in RAM to estimate quantiles. It may be | |
| 29 better to sample across all chromosomes so as not to lose any systematic differences between them - the current method will hide those | |
| 30 differences unfortunately. Sampling might be possible. Looking at the actual quantile values across a couple of test bigwigs suggests that | |
| 31 there is not much variation between chromosomes but there's now a tabular report to check them for each input bigwig. |