Dear Galaxy support team,
I’ve downloaded a bam file created on the Galaxy server using the tool bowtie2, and am now trying to upload it as a custom track on the UCSC genome browser. However, I’m getting the error that the bam index file (.bai) cannot be read. As far as I understood this index file was created, since I am able to display the bam file as a track through the UCSC link on the server.
Any suggestions on how to retrieve/download the bam index file?