Saving IGV images for bigwig files

Question

[Varun Gupta]

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

Answer 1

[Chris Miller]

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.

[erwan.scaon]

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.

Answer 2

[venu]

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.

[Varun Gupta]

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

[venu]

How did you install?

[Varun Gupta]

pip install pyGenomeTracks

[Varun Gupta]

It got installed here

/home/varun/.local/bin

[venu]

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

[Varun Gupta]

Hi 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??

[venu]

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.

Answer 3

[Friederike]

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

Answer 4

[dariober]

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).