IGV: first bases of each chromosomes missing when loading genome file

Question

[Pierre]

Hi,

I have a multifasta file of my genome sequence where chromosomes are named Chr1, Chr2, etc.

When I load this genome with IGV, the first base of chromosome 1 is missing, the 2 first bases of chromosome 2 are missing, 3 bases for chromosome 3, etc.

So when I load an annotation file everything is shifted.

This problem occurs with IGV 2.16, 2.17, 2.18.4 on Windows but not with IGV 2.18 for Linux (Ubuntu) with the exact same files.

Does anyone have any idea on how to solve that problem?

Thanks!

[GenoMax]

Can you post a screenshot of where you see this?

You may want to report this to IGV development team via IGV help forum: https://groups.google.com/g/igv-help

[Pierre]

Thanks for your reply, I'll report this.

For example, the chromosome 2 starts with this sequence:

>Chr2
cttaactttatatttttta...

But here is what IGV is displaying

Answer 1

[Pierre]

A solution was found : https://groups.google.com/g/igv-help/c/HKE4ISRlKxU

Answer 2

[Istvan Albert]

Check your file and line endings. It feels like there is some issue with Windows and UNIX line endings.

I checked on a MacOS, and by making the genome Windows line endings, I got an extra unspecified base before the first base.

[Pierre]

I have the same issue with Unix and MacOS line endings. With Windows line endings it's even worst.

When I change the names of the chromosomes from Chr1, Chr2, ... to ChrA, ChrB, ... everything is fine. So the problem comes from the chromosome names finishing with a number.

[Istvan Albert]

Internally IGV does remap chromosome names chr1 to 1 and even to NCBI style chromosome naming like NC_000001.11 and probably more names across the builds. Perhaps that remapping process is also going awry.

But yes, that you can't even trust IGV to show the correct coordinates ... that says so much about bioinformatics ... what hope is there for a reproducible analysis when you run into trouble with even the simplest visualizations? (rhetorical question :-/)