visibility range threshold

[Farzaneh Assadian]

Hi There,

I am using igv in the mac platform. I have mapped my miRNA sequencing results against EBV virus genome (170 Kb). I would like to see the global picture of the mapped miRNAs. I tried to change the visibility range threshold but for some reason it was not possible. Also the Ok tab although is hidden behind the panel! The change has been applied.

Currently I used igv 2.3.77 but I had the same issue with the older version too.

Could you please tell me how should I solve the issue?

Regards,

Farzaneh

[Jim Robinson]

Hi,

Could you provide more details?  Why was it not possible?  Perhaps some screenshots would help.

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[Farzaneh Assadian]

Hi Jim,

Thanks for replying. The weird thing is that the Ok and cancel buttons are first hidden (as you could see in the screenshot) and after some time the appear but it seems that they are deactivated. When I press Ok nothing happens! 

Also when trying to run the count command in igv tools it gives the null error massage.

Could it be igv memory issue?

Regards,

Farzaneh

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[Jim Robinson]

Hi Farzaneh,

That's strange, it could be a memory issue but I doubt it.   Could you provide details on your environment? Specifically

Hardware & operating system
How are you downloading & starting IGV (webstart, binary dist, something else)?

Also, send your igv.log file,  located in the igv folder under your home directory.

As a workaround for the preferences window button you can do the following.  First quit IGV, then open the file "prefs.properties" in the igv folder in a plain text editor and add the following line

SAM.MAX_VISIBLE_RANGE=200

The range is in kb.   Save the file and then start IGV.  Its important that you do this after shutting down IGV, otherwise it will get written over.

Jim

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