Issue with Bowtie2 and HISAT2

[jennaj]

Hi @smahavadi

If you didn’t find the problem yet, it may be that the genome is missing an index. Likely the samtools index.

Please see this prior Q&A and the one it links to for more details:

Reference Genome in some tools - Fully indexing genomes with Data Managers

Hi @tomlodz – just to add a bit to @wm75’s reply: To avoid problems, index reference genomes using the four primary Data Managers first (the sam index is included). This ensures basic functionality across tools, and Galaxy’s built-in functions, that do not have a tool-specific Data Manager. More help in the post below. It lists the four primary Data Managers that should be run on every genome and the order that tends to work best: These four can be run in a different order or after other too…

Best, Jen