Question: Saving IGV images for bigwig files
1
gravatar for Varun Gupta
9 months ago by
Varun Gupta1.1k
United States
Varun Gupta1.1k wrote:

Hi,

I have 100 bigwig files and a bed file which has 80 features. I want to load all the bigwig files and bed annotation file in IGV and for each feature I want to output an image which has for each feature all the loaded 100 bigwig files. In total I should have 80 graphs(for 80 features). Also I want it to scroll and not a screen shot as I want to see all the bigwig files. I am writing a batch script as told in IGV but I cannot get all the bigwig files to display.

Any help how to do it is appreciated.

Thanks

igv bigwig • 636 views
ADD COMMENTlink modified 9 months ago by dariober9.7k • written 9 months ago by Varun Gupta1.1k
2
gravatar for Chris Miller
9 months ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

You can do this with batch files in IGV. Here's a little wrapper script that automates some of it: https://github.com/chrisamiller/igvScreenshot

To be clear, I know you said no screenshots, but on a headless node, you can expand these to whatever height/size you want by tweaking params.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Chris Miller20k

In the "screenshot" categorie, check this paper : Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform. They have "created an IGV batch script to load the samples in which each variant was called", it's pretty nice.

ADD REPLYlink written 9 months ago by erwan.scaon570
1
gravatar for venu
9 months ago by
venu5.7k
Germany
venu5.7k wrote:

Recently I started using https://github.com/deeptools/pyGenomeTracks for a similar purpose. You can loop over all features or run in batch mode.

You have to spend some time configuring the input tracks file though.

ADD COMMENTlink written 9 months ago by venu5.7k

Hi venu, I downloaded and installed the pyGenomeTracks but I cannot locate make_tracks_file command for making the config file. Where does this go. I am using linux machine

ADD REPLYlink written 9 months ago by Varun Gupta1.1k

How did you install?

ADD REPLYlink written 9 months ago by venu5.7k
pip install pyGenomeTracks
ADD REPLYlink written 9 months ago by Varun Gupta1.1k

It got installed here

/home/varun/.local/bin
ADD REPLYlink written 9 months ago by Varun Gupta1.1k

Then add this directory to PATH. It will work smoothly.

ADD REPLYlink written 9 months ago by venu5.7k

enter image description hereHi Venu, I tried making plots by providing this command

./pyGenomeTracks --tracks tracks.ini --BED ~/test.bed -out fig_

The graph is showing too much upstream and downstream of my bed coordinates. Any way to fix that Also how can i display the name of the feature present in the bed file??

ADD REPLYlink modified 9 months ago • written 9 months ago by Varun Gupta1.1k

graph is showing too much upstream and downstream of my bed coordinates

I did not experience this. Explore the options (commented) in *.ini file. If I remember correctly, you should provide feature names in GFF format. Then it shows the feature name on plot.

ADD REPLYlink written 9 months ago by venu5.7k
0
gravatar for Friederike
9 months ago by
Friederike2.3k
United States
Friederike2.3k wrote:

the Bioconductor Gviz package will also do what you're looking for (allowing for Genome Browser style snapshots in a scripted manner)

ADD COMMENTlink written 9 months ago by Friederike2.3k
0
gravatar for dariober
9 months ago by
dariober9.7k
Glasgow - UK
dariober9.7k wrote:

In these cases, I cannot help mentioning my own tool, ASCIIGenome. It doesn't help with the question of how to do it with IGV, of course, but I would suggest that for batch processing it might be a better alternative (see examples here).

ADD COMMENTlink written 9 months ago by dariober9.7k
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