I am trying to align reads to the TAIR10 Arabidopsis genome with TopHat v2.1.0 (I have an old protocol that uses this suite), and was in fact successful at generating BAM files. However, when I go to download the BAI index files, I get a Server 500 error. The UUID for the 4 analyses are
8ad6c1a7-9995-471f-bd86-a1b9ed7ac4c2, ac84ffa3-c88c-4542-9574-150b9f3d0fa3, 8f54476a-aeaa-4cf4-8cd9-fe83988a6e0c, and 1394bae2-e0c9-4032-92a1-b77f3cef56f8.
I am not able to use the right side bar to view the BAM files in IGB either (presumably because the BAI files are missing/corrupted). I've seen in other posts that Galaxy is supposed to automatically generate BAI files but what to do if it doesn't? Editing the metadata seems to call up a JSON string with lots of parameters in it, many of which don't seem to belong to me. It would be nice to have samtools index function to be able to recreate these BAI if necessary. Am I missing something?