'Tracks' for translation reading frames spontaneously change order in different parts of genome

[ghous...@gmail.com]

Hello,

I couldn't find a prior answer to this, but apologies if it's already been asked. 

I am working with a reference genome (loaded into IGV from a multi fasta file). When I select 'Show translation' for the sequence, then scroll to different parts of the genome using a fairly zoomed-out view, the order of the three reading frames for the translation sometimes changes spontaneously (I am using IGV 2.4.4). Is there a reason for this? I am trying to map how the reading frame changes across exons of a long gene, and this spontaneous re-ordering of these 'tracks' makes that much more difficult.

Is there any way to 'lock' the order of these reading frame displays?

Thank you all very much for any insights or help you can give me about this,

Geoffrey

[James Robinson]

Hi,

The reading frames have no connection to any annotation,   I'm trying to envision what you are doing but can't.   How do you determine order?   It would be helpful if you could describe order with referencing annotations,  if you removed the gene track the frames would still be there.

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[James Robinson]

Sorry that's "without referencing annotations"

[ghous...@gmail.com]

Thank you very much for your quick reply, and I'm sorry if parts of my original message were unclear.

I only have the genome sequence loaded (not any annotation tracks), and I'm looking at the three reading frames provided for that sequence (and its given orientation).  By "order" of the reading frame 'tracks' (maybe referring to these as 'ribbons' instead is more accurate because they are not actual IGV 'tracks'), I mean the stacking order of the three possible translations 'ribbons' - for example, currently when I scroll to different parts of the genome in a fairly zoomed-out view, the reading frame that previously was shown as the top 'ribbon' is now displayed either as the middle or the bottom 'ribbon', and the order changes dynamically as I scroll left/right through the genome. 

From what I can tell, this ordering does not seem to correspond to particular regions or characteristics of the genome, because if I scroll enough times left/right in the same region, each 'ribbon' can appear on the top, middle or bottom of the three, but any given instance of this scrolling doesn't seem to guarantee the same re-ordering.

Thank you for any insights you have about this, and for any possible ways to maintain the order of these 'ribbons'.

Cheers,

Geoffrey

[ghous...@gmail.com]

Here is an image of what I was trying to describe with the different ordering of reading frame 'ribbons' caused by scrolling left/right if it helps. The arrow's pointing to the same 'ribbon' each time, but its order changes.

Thanks for any suggestions you have,

Geoffrey

[James Robinson]

Ah, ok, I got it.   So there is nothing you can do about this right now but I will look into making them stable.   The order, of course, is arbitrary but I can see how stability would be desirable.    If you are able open a github issue on this and you can track progress on the issue, but I will look into it regardless.

Jim

[James Robinson]

I've made a change that should stablize the frames in a fixed order.   It will be available in the next point release,  2.4.16.   If you need it in the meantime you can use the development "snapshot" version that is built nightly:  http://software.broadinstitute.org/software/igv/download_snapshot

[ghous...@gmail.com]

Hi Jim,

Thank you very much for your fast responses and for addressing this extremely quickly! I really appreciate your help with this - I'll try the development 'snapshot' version that you linked.

Thanks again,

Geoffrey

[James Robinson]

You're welcome.   Please let me know if you find problems,   I did some testing but obviously not a huge amount.

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