Create README.md

hubs/ashm_hubs/README.md

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+# Mutation pattern browsers for GAMBL
+
+```
+  /$$$$$$     /$$$$$$    /$$      /$$   /$$$$$$$    /$$. 
+ /$$__  $$   /$$__  $$  | $$$    /$$$  | $$__  $$  | $$. 
+| $$  \__/  | $$  \ $$  | $$$$  /$$$$  | $$  \ $$  | $$. 
+| $$ /$$$$  | $$$$$$$$  | $$ $$/$$ $$  | $$$$$$$   | $$. 
+| $$|_  $$  | $$__  $$  | $$  $$$| $$  | $$__  $$  | $$. 
+| $$  \ $$  | $$  | $$  | $$\  $ | $$  | $$  \ $$  | $$. 
+|  $$$$$$/  | $$  | $$  | $$ \/  | $$  | $$$$$$$/  | $$$$$$$$. 
+ \______/   |__/  |__/  |__/     |__/  |_______/   |________/. 
+~~GENOMIC~~~~~~~~~~~~~OF~~~~~~~~~~~~~~~~~B-CELL~~~~~~~~~~~~~~~. 
+~~~~~~~~~~~~~ANALYSIS~~~~~~MATURE~~~~~~~~~~~~~~~~~~~LYMPHOMAS~. 
+```
+
+## What data are available
+
+Currently, there is a single browser hub that provides access to the anonymized mutations from the genomes in GAMBL subset to the regions we identified as being recurrently affected by aSHM. There are separate tracks for CLL, Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL). For DLBCLs, mutations are coloured according to the LymphGen class of that patient as determined from their genome-wide mutation profile. For BLs, we instead use the genetic subgroup described in Thomas et al. The colour key we use can be found [here](https://morinlab.github.io/LLMPP/colours.html). Additional hubs with more informative colour schemes for other entities are in the works. 
+
+## How to visualize on UCSC
+
+Navigate to the [UCSC genome browser](http://genome.ucsc.edu/cgi-bin/hgGateway) and make sure hg19 is selected. Enter any gene of interest into the search box. If you don't have a favourite gene, you can enter *EZH2*. For a shortcut, you can also use [this link](https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr18%3A60977274-60991908) to jump directly to the BCL2 locus. Once you are in the genome browser, select the _Track Hubs_ option in the _My Data_ menu at the top. This should bring you to the Track Hubs menu. Select the middle tab, as shown in the screenshot below. 
+
+<img src="https://github.com/morinlab/LLMPP/blob/main/hubs/ashm/etc/ucsc_1.png?raw=true"  width="800">
+
+Copy [this url](https://raw.githubusercontent.com/morinlab/LLMPP/main/hubs/ashm/hub.txt) to your clipboard and paste it into the box to the right of *URL* and click _add hub_. This should bring you back to the browser with the custom tracks now shown. If you don't see anything you may need to navigate to a different region. 
+Try pasting this region into the navigation box: `chr6:37,136,653-37,141,935` or, to reproduce the image below, use `chrX:12,993,029-12,995,149`
+
+<img src="https://github.com/morinlab/LLMPP/blob/main/hubs/ashm/etc/ucsc_2.png?raw=true"  width="800">
+
+To view a region that is more abundantly mutated in BL, try perusing the BACH2 locus (example below). 
+
+<img src="https://github.com/morinlab/LLMPP/blob/main/hubs/ashm/etc/ucsc_3.png?raw=true"  width="800">
+
+
+## How to visualize in IGV
+
+The repository contains bed files that can be loaded in IGV (in the `bed_format` directory). If you download or clone the repository (via the links on the [main page](https://github.com/morinlab/LLMPP)), you can load those into IGV individually by navigating to that folder within IGV. You can also open the xml file as an IGV session. 
+
+<img src="https://github.com/morinlab/LLMPP/blob/main/hubs/ashm/etc/igv_screenshot.png?raw=true"  width="800">
+