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planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
author fubar
date Mon, 01 Jul 2024 03:08:11 +0000
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c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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1 ## bigwig peak outlier to bed
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c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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3 ### July 30 2024 for the VGP
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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.
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7 The next JBrowse2 tool release will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below.
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9 ### Find and mark BigWig peaks to a bed file for display
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11 In the spirit of DeepTools, but finding contiguous regions where the bigwig value is either above or below a given centile.
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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)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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14 ![image](https://github.com/fubar2/bigwig_peak_bed/assets/6016266/cdee3a2b-ae31-4282-b744-992c15fb49db)
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16 ![image](https://github.com/fubar2/bigwig_peak_bed/assets/6016266/59d1564b-0c34-42a3-b437-44332cf1b2f0)
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18 Big differences between chromosomes 14,15,21,22 and Y in this "all contigs" view - explanations welcomed:
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20 ![image](https://github.com/fubar2/bigwig_peak_bed/assets/6016266/162bf681-2977-4eb8-8d6f-9dad5b3931f8)
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23 [pybedtools](https://github.com/jackh726/bigtools) is used for the bigwig interface. Optionally allow
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24 multiple bigwigs to be processed into a single bed - the bed features have the bigwig name in the label for viewing.
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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26 ### Note on quantiles per chromosome rather than quantiles for the whole bigwig
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28 It is just not feasible to hold all contigs in the entire decoded bigwig in RAM to estimate quantiles. It may be
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29 better to sample across all chromosomes so as not to lose any systematic differences between them - the current method will hide those
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30 differences unfortunately. Sampling might be possible. Looking at the actual quantile values across a couple of test bigwigs suggests that
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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31 there is not much variation between chromosomes but there's now a tabular report to check them for each input bigwig.