unable to load bam files

[G M]

Dear igv help desk, 

I have been using IGV_2.19.7 on mac OS Sequoia 15.6.1. 

The reference genome is downloaded from hosted genome... and is A. thaliana (TAIR10)

Since yesterday, for unknown reasons, I cannot load my local bam files. 

I always get the error message:

does not contain any sequence names which match the current genome (see screenshot)

whatever the bam file (associated with its bai file) that I am trying to upload and that usually work just fine. 

Looking forward to hearing from you. 

Best, 

Guillaume

[igv-help]

Hmm. IGV's genome definition for TAIR10 includes a file that provides aliases for the chromosome names. So for example the sequence has the NC_* notation, but the alias file tells IGV other corresponding names e.g. chr1, 1, etc.  Perhaps the connection to that file was down temporarily.  

Can you try again and see if it's still not working. 

If not, try selecting TAIR10  again from Genomes > Download Hosted Genome (i.e. don't just select it from the IGV dropdown menu).

If the alias file is working, you should see chr1, chr2, etc in the IGV chromosome dropdown menu.

Helga

[G M]

Dear Helga

Thanks for your answer. 

I tried what you suggested, I downloaded TAIR10 genome (download sequence and download annotations) but unfortunately, I still get the same error message. I really don't know what to do...

Best, 

Guillaume 

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[igv-help]

Hi Guillaume,

I didn't mean to make you download the whole sequence and annotations. I apologize for not being sufficiently clear on that. I just mean select it again from the Genomes menu.

Can you send me the following:

1) The contents of the IGV log from a run where this is failing. The log file is located in the "igv" folder in your user home and probably named igv0.log.

2) The contents of the tair10.json file which should be located in the "genomes" subfolder under "igv"

Helga

[G M]

Hi Helga, 

I found these 2 files. I hope that can help... Thanks!

Best, 

Guillaume

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[igv-help]

I figured out the problem. According to the error message, your BAM file contains chromosome names "Chr1", "Chr2", etc. The chromosomes in the TAIR10 genome are named "NC_003070.9", "NC_003071.7", etc. As I previously said, IGV uses an alias file for the most common alternative names, but it does not include the "Chr*" notation with a capital C. IGV retrieves the genome data including the alias file from the UCSC site. 

But here's a workaround. You can update the alias file for the genome that you downloaded.  In your genomes folder there is now a subfolder named "tair10". Replace the file that is named GCF_000001735.3.chromAlias.txt file with the updated file that I've attached here. Note that the file name has to be the same as it was (or you can edit the tair10.json file to refer to a file with the name of your new file).  

I don't know if you created the BAM files yourself, but the best way to avoid this problem is to make sure that the reads are aligned to a FASTA file with standard names.

Helga

[G M]

Hi Helga, 

Thank you so much! It is working fine now! 

I can see that in the updated file you added a tab with Chr numbers, I guess that was the trick! 

What I still don't understand is why our bam files - that indeed we generated ourselves- used to work just fine before... 

Anyhow, I have transferred your comments to my colleague Nathalie who is doing our bioinfo analyses and we will discuss more about this issue together. 

Again, thank you very much for your help!

All the best, 

Guillaume

To view this discussion visit https://groups.google.com/d/msgid/igv-help/cc09e4e2-bacf-4a52-807b-1fa9bbf23fe7n%40googlegroups.com.

[igv-help]

Hi,

We are transitioning over time from our custom hosted genome files to standard files hosted at UCSC.  If your files worked previously,  I suspect that capitalized chromosome names were included in previous ad-hoc alias files we might have created.  I do recommend you standardize your chromosome / sequence names,  you might have problems with other tools with the capitalized names.  For example, I doubt they will be recognized by UCSC if you should wish to view them there.

Best,

Jim

[G M]

Hi Jim,

Thanks for the heads up and advices!

We will keep that in mind. 

Best,

Guillaume 

To view this discussion visit https://groups.google.com/d/msgid/igv-help/96a43a28-dc0b-41d3-b21b-f45f01250f21n%40googlegroups.com.