Question about inserted bases

[ryo...@gmail.com]

I have a question about viewing alignments. How to view the inserted bases?

In version 2.4.19, I can see the inserted bases like insertion(2bases):AT by hovering over the insertion symbol.

However, after version 2.6(eg, version 2.7.2), the inserted bases are not shown.

I use Windows10 (version1903).

Please let me know if it is a bug or a way to improve it.

[Helga Thorvaldsdottir]

Hi,

You can control the popup behavior via the yellow balloon icon in the toolbar (to the left of the zoom slider).

Check to see if it is set to either "Show details on click" or "Never show details". 

If it's set to "Show details on click" then you can click on the insertion symbol to see the bases.

If you prefer the hover behavior, just set it to "Show details on hover". 

Helga

[ryo...@gmail.com]

I can see yellow balloon icon, but inserted bases are not shown after IGV version 2.5.

Is it possible to show?

[Helga Thorvaldsdottir]

Hi,

It works in the test cases I've tried. Can you send us a small sample file? You can extract a region of your current file with samtools, or with IGV itself. To use IGV, zoom the view to a region that includes the insertions in question, then right-click and select "Export alignments". It will create a .sam file that you can send us. If you have problems attaching the file to this thread, you can send it to us at igv-...@broadinstitute.org.

Helga

[Helga Thorvaldsdottir]

Hi - we tried the test file you sent us and we still see the inserted base in IGV 2.7.2, so it's still a mystery. 

To help us further investigate, can you send us more information:

1) Find your IGV prefs.properties file (it's in the igv folder in your home directory, unless you've directed IGV to move it somewhere else). Please send us the whole file (it's small) 

2) In IGV, find a read with an insertion that has the problem; right-click on the read and select "Copy read details to clipboard"; paste the details into a text file. Please also send us that file.

Helga

[Ryo FUTAHASHI]

 prefs.zip

Dear Helga,

Here I am attaching two files.

Does a prefs.properties file mean prefs.dll?

1) Find your IGV prefs.properties file (it's in the igv folder in your home directory, unless you've directed IGV to move it somewhere else). Please send us the whole file (it's small) 

2) In IGV, find a read with an insertion that has the problem; right-click on the read and select "Copy read details to clipboard"; paste the details into a text file. Please also send us that file.

Best regards,

Ryo

2019年11月23日(土) 5:45 Helga Thorvaldsdottir <he...@broadinstitute.org>:

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[James Robinson]

Hi,

No we do not mean prefs.dll,  we mean prefs.properties.  Its in the igv folder in your user home directory.

You didn't send us the complete text the "read details", but I was able to find the read in question from the sequence.   We can't reproduce the problem,  you can see below what I see.   If you send prefs.properties we will see if anything in there is causing this,  otherwise I don't have an answer.

[Ryo FUTAHASHI]

Here I am attaching the prefs.properties file.

I hope you can find the cause of our problems...

2019年11月26日(火) 7:57 James Robinson <jrob...@broadinstitute.org>:

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