Trying to make a custom GBrowse track from a BAM file

Model Organism: Worms Scientific Discussion
1

Hello Wormbasers!

I have a bit of a beginners bioinformatics question.
I want to examine some sequence reads in Wormbase GBrowse. I have them as a fastq file, and converted them to a BAM file, by running it through RNA STAR on the Galaxy platform.
There is a help page on wormbase (https://wormbase.org/gbrowse-static/annotation_help.html) that mentions BAM files can be uploaded as custom tracks, but when I try to do so I keep getting errors.

Any suggestions on what I might be doing wrong? I think either my BAM file is not what it should be, or there might be some step I am missing because I am unaware of it.

2

To see whether it is a problem with the file, I suggest trying

https://genome.ucsc.edu/cgi-bin/hgCustom?hgsid=1065500785_AHWN8mXwEmypiUFvnQajVOd5hXyZ

or

https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

And as on Wormbase, GBrowse has not been supported for some time, it is best to use JBrowse. Under “File” => “Open track file or URL”