diff README.md @ 6:eb17eb8a3658 draft

planemo upload commit 1baff96e75def9248afdcf21edec9bdc7ed42b1f-dirty

--- a/README.md	Mon Jul 01 05:02:05 2024 +0000
+++ b/README.md	Tue Jul 23 23:12:23 2024 +0000
@@ -1,10 +1,10 @@
-## bigwig peak outlier to bed
+## 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.
+This is a Galaxy tool, for building some of the [NIH MARBL T2T assembly polishing](https://github.com/marbl/training) tools as Galaxy workflows.
 
-The next JBrowse2 tool release will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below.
+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
 
@@ -29,3 +29,69 @@
 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.
+
+### Table reports
+
+The optional table output report gives a crude histogram and the top/bottom 10 values to help 
+understand what is likely to be informative. In this example, there are 26700 zero values so
+using a lower cutoff quantile is likely to have a lot of them, although a large window requirement
+will decease the overload...
+
+Descriptive measures
+bigwig  test
+contig  chr10_PATERNAL
+n       135711693
+mean    12.178164
+std     7.997467
+min     0.000000
+max     365.000000
+qtop    364.00
+qbot    noqlo
+First/Last 10 value counts
+Value   Count
+0.00    26700
+1.00    82900
+2.00    261400
+3.00    676993
+4.00    1665500
+5.00    3125700
+6.00    5078000
+7.00    7469000
+8.00    10191700
+9.00    12544600
+355.00  100
+356.00  100
+357.00  300
+358.00  100
+360.00  500
+361.00  300
+362.00  200
+363.00  600
+364.00  900
+365.00  700
+Histogram of bigwig values
+chr10_PATERNAL        18.25 | 127,047,593 | **************************************************************************
+chr10_PATERNAL        36.50 |   7,510,000 | ****
+chr10_PATERNAL        54.75 |     818,900 |
+chr10_PATERNAL        73.00 |     117,200 |
+chr10_PATERNAL        91.25 |      51,900 |
+chr10_PATERNAL       109.50 |      44,200 |
+chr10_PATERNAL       127.75 |      21,600 |
+chr10_PATERNAL       146.00 |      17,900 |
+chr10_PATERNAL       164.25 |      16,400 |
+chr10_PATERNAL       182.50 |      18,600 |
+chr10_PATERNAL       200.75 |       5,400 |
+chr10_PATERNAL       219.00 |       6,600 |
+chr10_PATERNAL       237.25 |       6,200 |
+chr10_PATERNAL       255.50 |       3,900 |
+chr10_PATERNAL       273.75 |       4,500 |
+chr10_PATERNAL       292.00 |       7,100 |
+chr10_PATERNAL       310.25 |       3,000 |
+chr10_PATERNAL       328.50 |       2,700 |
+chr10_PATERNAL       346.75 |       3,500 |
+chr10_PATERNAL       365.00 |       4,500 |
+chr10_PATERNAL ------------ |------------ |
+chr10_PATERNAL           N= | 135,711,693 |
+chr10_PATERNAL ------------ |------------ |
+
+