IGV view of bam file

Question

[biolab]

Hi, everyone,

I have a small problem regarding to saving the image of IGV viewing of bam file. IGV has squashed and expanded options for viewing mapping reads. My interesting gene has many reads. If using the squash option, the image has low resolution, but when choosing expanded option, I cannot get an image including all reads.

Your comments or answers will be highly appreciated. THANKS!

Answer 1

[thackl]

IGV can also save to .svg vector graphic (which is easily converted to pdf or so). That way resolution wouldn't matter.

[biolab]

Hi, thackl, thank you for your reply. The .svg saving option is very useful! However, my problem has not been resolved. I used File->Save image.., and then got the following image. I would like to get all reads. Do you have any suggestions? THANKS!

[biolab]

My IGV image is like follows. There are more reads outside of the image. I want to get all reads inside an image. THANK YOU for your attention.

-----------------------------------------------
|<-----------------------                     |
|<-----------------------                     | 
|    <-----------------------                 |
|              <-----------------------       |
-----------------------------------------------

[thackl]

Are you using squashed/collapsed view and not all of your reads fit within your screen?

[biolab]

Yes, thackl, exactly. I need to get an image with all reads in. THANKS!

[thackl]

There is one very, very ugly way that would work if you need just one picture (fyi, I can fit up to 700X in a regular picture, how much coverage do you have? You might want to think about igvs read subsampling option for displayed reads: Preferences->Alignment->subsample I think).

Use IGV in windowed mode (not fullscreen), move the window to the bottom of your screen until most of its is outside the screen, than extend the window by dragging the top bar to the top of your screen, if necessary, repeat - as I said, very ugly. If you take a picture, it will cover the entire window including the invisible parts "below" your screen and thus include reads at very high coverages..

[biolab]

Hi thackl,thank you very much for your detailed method. I used photoshop to merge three pieces into one, which looks fine. THANKS.

Answer 2

[Alternative]

You can change the visibility range threshold in "Alignments" section of "Preferences". Set it to a size higher than your gene of interest and you will get all reads included.

[biolab]

Thank you, Pierre. Your answer is very helpful!