Mercurial > repos > fubar > bigwig_outlier_bed

comparison README.md @ 6:eb17eb8a3658 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 1baff96e75def9248afdcf21edec9bdc7ed42b1f-dirty
author fubar
date Tue, 23 Jul 2024 23:12:23 +0000
parents c71db540eb38
children
comparison
equal deleted inserted replaced
5:68cb8e7e266b 6:eb17eb8a3658
1 ## bigwig peak outlier to bed 1 ## bigwig peak bed maker
2 2
3 ### July 30 2024 for the VGP 3 ### July 30 2024 for the VGP
4 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. 5 This is a Galaxy tool, for building some of the [NIH MARBL T2T assembly polishing](https://github.com/marbl/training) tools as Galaxy workflows.
6 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. 7 JBrowse2 2.12.3 update will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below.
8 8
9 ### Find and mark BigWig peaks to a bed file for display 9 ### Find and mark BigWig peaks to a bed file for display
10 10
11 In the spirit of DeepTools, but finding contiguous regions where the bigwig value is either above or below a given centile. 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) 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)
27 27
28 It is just not feasible to hold all contigs in the entire decoded bigwig in RAM to estimate quantiles. It may be 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 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 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. 31 there is not much variation between chromosomes but there's now a tabular report to check them for each input bigwig.
32
33 ### Table reports
34
35 The optional table output report gives a crude histogram and the top/bottom 10 values to help
36 understand what is likely to be informative. In this example, there are 26700 zero values so
37 using a lower cutoff quantile is likely to have a lot of them, although a large window requirement
38 will decease the overload...
39
40 Descriptive measures
41 bigwig test
42 contig chr10_PATERNAL
43 n 135711693
44 mean 12.178164
45 std 7.997467
46 min 0.000000
47 max 365.000000
48 qtop 364.00
49 qbot noqlo
50 First/Last 10 value counts
51 Value Count
52 0.00 26700
53 1.00 82900
54 2.00 261400
55 3.00 676993
56 4.00 1665500
57 5.00 3125700
58 6.00 5078000
59 7.00 7469000
60 8.00 10191700
61 9.00 12544600
62 355.00 100
63 356.00 100
64 357.00 300
65 358.00 100
66 360.00 500
67 361.00 300
68 362.00 200
69 363.00 600
70 364.00 900
71 365.00 700
72 Histogram of bigwig values
73 chr10_PATERNAL 18.25 | 127,047,593 | **************************************************************************
74 chr10_PATERNAL 36.50 | 7,510,000 | ****
75 chr10_PATERNAL 54.75 | 818,900 |
76 chr10_PATERNAL 73.00 | 117,200 |
77 chr10_PATERNAL 91.25 | 51,900 |
78 chr10_PATERNAL 109.50 | 44,200 |
79 chr10_PATERNAL 127.75 | 21,600 |
80 chr10_PATERNAL 146.00 | 17,900 |
81 chr10_PATERNAL 164.25 | 16,400 |
82 chr10_PATERNAL 182.50 | 18,600 |
83 chr10_PATERNAL 200.75 | 5,400 |
84 chr10_PATERNAL 219.00 | 6,600 |
85 chr10_PATERNAL 237.25 | 6,200 |
86 chr10_PATERNAL 255.50 | 3,900 |
87 chr10_PATERNAL 273.75 | 4,500 |
88 chr10_PATERNAL 292.00 | 7,100 |
89 chr10_PATERNAL 310.25 | 3,000 |
90 chr10_PATERNAL 328.50 | 2,700 |
91 chr10_PATERNAL 346.75 | 3,500 |
92 chr10_PATERNAL 365.00 | 4,500 |
93 chr10_PATERNAL ------------ |------------ |
94 chr10_PATERNAL N= | 135,711,693 |
95 chr10_PATERNAL ------------ |------------ |
96
97