Jbrowse reference sequence issue

Question

[alslonik]

Hi all.

I am trying to look at my newly assembled genome with jbrowse, which is comprised of chromosomes and of short contigs as well. Chromosomes are called Chr1, Chr2 etc, contigs have numeric names - 1 to N... When I load the fasta file onto my jbrowse as a refseq, and choose "Chr1" on the dropdown menu, it automatically jumps to contig "1".. I have the option to rename the contigs 1-9, but that means that i will need to make corrections to so many files, or re-run so many scripts, which i already run with the original names...

I am guessing that there it is something to deal with aliases, maybe? But i cannot find anything helpful on the jbrowse documentation... Hoping that someone will know the answer... Thanks!

[GenoMax]

tagging: cmdcolin developer of Jbrowse.

Answer 1

[cmdcolin]

if you use the option exactReferenceSequenceNames it will fix it https://jbrowse.org/docs/global_options.html

to enable, try adding

exactReferenceSequenceNames=true

to jbrowse.conf

[cmdcolin]

@GenoMax thanks for tagging me!

[alslonik]

Brilliant! Thank you!