Missing bam index when downloading bam file

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?


When you clicked on the download icon on your Galax dataset, you should have been presented with a small select menu offering to download the dataset OR its bam_index. So just go to Galaxy again, grab the index file and place it next to your downloaded BAM file. Make sure both files have the same basename with .bai added to the index.

Found it, thanks!