disappearing features in IGV

[Mark Rose]

Hi All

I am having a problem when displaying bedgraph files in IGV.  I've attached an image which illustrates it.  Basically, features are present or not depending on the zoom level.  Now I could understand this if it were like the behavior of nucleotide sequence (i.e. it is only shown above a certain zoom level).  However, some features in multiple bedgraph files appear at a low zoom level, disappear at a higher zoom level, and then sometimes reappear at a still higher zoom level.  Is this to be expected and, if so, why? If not, any ideas what is wrong.

Thanks for your help

[James Robinson]

What version of IGV are you using?  You can determine this from "Help > About".

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/8594fae3-b673-4b59-964f-790d9ae6f4d1%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Mark Rose]

Version 2.3.75 (112)

On Wednesday, November 2, 2016 at 12:57:22 PM UTC-4, Jim Robinson wrote:

What version of IGV are you using?  You can determine this from "Help > About".

On Wed, Nov 2, 2016 at 8:50 AM, Mark Rose <mark...@syngenta.com> wrote:

Hi All

I am having a problem when displaying bedgraph files in IGV.  I've attached an image which illustrates it.  Basically, features are present or not depending on the zoom level.  Now I could understand this if it were like the behavior of nucleotide sequence (i.e. it is only shown above a certain zoom level).  However, some features in multiple bedgraph files appear at a low zoom level, disappear at a higher zoom level, and then sometimes reappear at a still higher zoom level.  Is this to be expected and, if so, why? If not, any ideas what is wrong.

Thanks for your help

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

[James Robinson]

Try updating and see if the problem remains.  

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/aee1645c-fc93-4929-bcc1-be76a77a6991%40googlegroups.com.

[Mark Rose]

Tried version 2.3.86, problem persists.

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/MQkzIW_TWHA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpsRjVnrd8UTikUdRU1bdgEWBWMa-YB03Sp_1GF7QaAW2w%40mail.gmail.com.

[James Robinson]

I'll need to see the file then,  can you create a small one that reproduces the problem, or point me to a downloadable file that does?

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAJFKk9BByccHrAtTJmct22Rey9X-gbFm5bQm8Y1%3Dor%2BH9CNmaQ%40mail.gmail.com.

[Mark Rose]

Here you go.  Among the features that display this behavior is one at position 1444.

Thanks for your help

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2Bpv5K%2BVc6AdjD-Eyk7cWWgtz6M2dWMYpWEbNrAfBp4MR2A%40mail.gmail.com.

[James Robinson]

Ok, that was helpful.  I found the problem.   The last (right-most) feature  in view of a bedgraph or wig file would sometimes be trimmed inappropriately before drawing.   You would only notice this with very sparse bedgraph or wig files, such as yours.   I've deployed a fix, it will be available later this evening as 2.3.87.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAJFKk9CgXZVdksu7X2w8FxLbiW_iH1KKr5cTf2zaGKpSXwCgFw%40mail.gmail.com.

[Mark Rose]

Great! I eagerly await it.  Thanks a lot for such a quick fix

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2Bpuz%2BecV7KDd%3D2ncaHDHh-LkuyugMVAUskrLv%2BwbduYedg%40mail.gmail.com.

[James Robinson]

Mark, this should be fixed now.   The version is 2.3.87.   

[mtr...@mindspring.com]

It is.  Much thanks.