Ask Your Question

Can't get plot to display

asked 2016-05-11 13:08:21 -0600

Whit Athey gravatar image

I am trying to display and compare two mtDNA sequences and also the reference sequence. The reference sequence is showing just fine, but the plots for my two BAM files are blank. Since the reference sequence is showing individual bases, I assume my scale is okay. The two files seem to load okay, and the titles of the files are showing, but no data. How do I get the plot to show up?

edit retag flag offensive close merge delete


According to the company that produced the above-mentioned mtDNA BAM files, the read depth is about 2000X. Is that too much to be displayed in the GH browser? Could that be causing the problem?

Whit Athey ( 2016-05-12 12:31:55 -0600 )edit

1 answer

Sort by ยป oldest newest most voted

answered 2016-05-12 15:52:54 -0600

Hi Whit,

I am sorry you are having issues visualizing your data in GenomeBrowse.

With mitochondrial data on the GRCh37 genome you will need to make sure you have the correct reference assembly specified in the drop down at the top of the GenomeBrowse window that matches the chromosome naming convention for this region. In particular, for the hg19 version of the assembly chrM is used to define this region but for the g1k version of the assembly chrMT is used.

If you click on the name of your BAM file in the GenomeBrowse plot and then scroll to the bottom of the Console window you will see how this region is identified in your BAM file. Should look similar to the below screenshot.

image description

So you will want to make sure and select the appropriate assembly for your data. If that does not work to fix the visibility can you try deleting the index file (BAI) that should be in the same directory as the BAM file? GenomeBrowse will then try and recompute the file if there are issues with the data you should get some error messages that may help diagnose what is going wrong. Screenshots of any error messages would be most useful.

The read depth of the data should not cause this issues, when the number of reads exceeds what can be rendered you will still see those that fit you will just get and error message saying not all reads could be drawn.

Let me know how I can help you further.

Thanks, Jami...

edit flag offensive delete link more


I can now see both files displayed as they should be. It apparently did have something to do with the reference, but it wasn't clear just what. I removed the hg19 reference and put in the g1k reference, but at first nothing happened. Then I swapped them again and it started working with either.

Whit Athey ( 2016-05-13 12:22:04 -0600 )edit

And, I can now have both references displayed without killing the display of my data. I'm not sure I understand what's going on, but I have obtained the information I was looking for. Thanks!

Whit Athey ( 2016-05-13 12:24:00 -0600 )edit
Login/Signup to Answer

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

Question Tools

1 follower


Asked: 2016-05-11 13:08:21 -0600

Seen: 377 times

Last updated: May 12 '16