I don't know how to make this bioinformatic picture

Question

[younglin113]

I saw this picture in a recent article. I thought it succinct and I also want to learn to make one. But I don't know what tools I should use to make it. Is there anyone can help me? Here is the picture:

[Devon Ryan]

Looks like a screenshot from the UCSC genome browser.

[younglin113]

Thanks a lot for your answer!!

[Michael]

Please make sure the link is correct and accessible openly, we can't see it.

[younglin113]

sorry, the link has been updated.

Answer 1

[Alex Reynolds]

I posted a Python-based tool on Github called soda.py that creates a web-ready gallery of UCSC browser shots. You just give it your BED file of coordinates, build, and session ID, and you specify an output directory where PDF and PNG results get stored (as well as an index.html file that lets you browse through snapshots with a web browser).

If you want to do things by hand, you can do something like the following quick and dirty approach to get a nice PNG. You'll need ImageMagick convert installed in order to convert the PDF to PNG. You'll also need GNU wget to do web requests on the command line.

$!/bin/bash

chrom="chr1"
chromStart=1234567
chromEnd=1234987
sessionID=1234
genomeBrowserURL="genome.ucsc.edu"
dumpURL="http://${genomeBrowserURL}/cgi-bin/cartDump"
postData="hgsid=${sessionID}&hgt.psOutput=on&cartDump.varName=position&cartDump.newValue=${chrom}%3A${chromStart}-${chromEnd}&submit=submit"
wgetOpts="--no-directories --recursive --convert-links -l 1 -A hgt_*.pdf"
wgetWaitOpts="--wait=1 --random-wait --tries=2 --timeout=100"
wget ${wgetWaitOpts} --post-data "${postData}" "${dumpURL}"
wget ${wgetOpts} ${wgetWaitOpts} "$url&position=${chrom}%3A${chromStart}-${chromEnd}" 2> fetch.log
mv hgt_*.pdf ${sessionID}.pdf
convert -density 300 ${sessionID}.pdf -background white -flatten ${sessionID}.png

You'd fill out chrom, chromStart, chromEnd and sessionID. Or use placeholders $1 etc. and pass them in on the command line.

If you have a few regions to look at, this would just be a matter of modifying this approach to loop over their respective chromosome name and interval values, and naming the output files appropriately. (Or you can use soda.py for automation.)

[Philipp Bayer]

If your species is not in the UCSC browser, you can make very similar density plots using KaryoploteR: https://bernatgel.github.io/karyoploter_tutorial/

[younglin113]

It really helps a lot, thanks for your help!

[Kevin Blighe]

Please up-vote answers and comments that have helped. Thanks!

[Alex Reynolds]

You're welcome - happy to help!

Answer 2

[shoujun.gu]

Its a typical genome browser visualization. You can get this kind of visualization in any genome browser.

Under the hood, it’s just a histogram. If you have the data, you can make these plots by any data visualization tools, there are various modules in python, R or JavaScript.