Question: Saving IGV images for bigwig files
1
gravatar for Varun Gupta
21 days ago by
Varun Gupta940
United States
Varun Gupta940 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 • 188 views
ADD COMMENTlink modified 20 days ago by dariober8.6k • written 21 days ago by Varun Gupta940
2
gravatar for Chris Miller
21 days ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k 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 21 days ago • written 21 days ago by Chris Miller19k

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 20 days ago by erwan.scaon410
1
gravatar for venu
21 days ago by
venu4.8k
Germany
venu4.8k 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 21 days ago by venu4.8k

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 21 days ago by Varun Gupta940

How did you install?

ADD REPLYlink written 21 days ago by venu4.8k
pip install pyGenomeTracks
ADD REPLYlink written 21 days ago by Varun Gupta940

It got installed here

/home/varun/.local/bin
ADD REPLYlink written 21 days ago by Varun Gupta940

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

ADD REPLYlink written 21 days ago by venu4.8k

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 21 days ago • written 21 days ago by Varun Gupta940

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 21 days ago by venu4.8k
0
gravatar for Friederike
21 days ago by
Friederike1000
United States
Friederike1000 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 21 days ago by Friederike1000
0
gravatar for dariober
20 days ago by
dariober8.6k
Glasgow - UK
dariober8.6k 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 20 days ago by dariober8.6k
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