Question: Problem with IGV - matching heading to reference genome
gravatar for blur
3.9 years ago by
European Union
blur20 wrote:


I am trying to see BAM files on IGV - but since the reference file has names that look like this: ca21chr1...

and the BAM file has headings that look like this: contig222, contig34 etc, it can't open the file to view the


I opened the file in BAMseek - and it is clear that the for each read, the right location on the reference was

found, but this is not read well in IGV.

Can anyone tell me how to change the headings to match the appropriate reference location?


Thank you!

igv galaxy • 868 views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by blur20
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Using the same exact reference dataset for all functions is very important - not only in Galaxy but across external applications. Changing BAM datasets will not solve the issue - or rather, is tedious and unless the references genomes are an exact match in all ways except for the chromosome identifiers, this will not be possible anyway. The simplest way forward is to add the reference genome used for the mapping to any visualization applications instead.

Would Trackster (under "Visualization" be an alternative that would work for you)? If you really want to use IGV, you can review the documentation for that application and add in your reference genome there as well in a local copy.

Help for using a Custom Reference Genome in Galaxy will help with using Trackster. Once the reference genome used for the mapping steps is loaded (in fasta format), continue on with the Custom Build set-up (under User -> Custom Builds) and assign the database (dbkey) metadata to the datasets. All instructions for these procedures are in our wiki here:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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