Just a quick note, I think there is a slight mistake in the directions here KneadData – The Huttenhower Lab for acquiring the human database. The command given on the page says “–download human bowtie2 $DIR” and this results in an error that one must select an available database. I looked around online and saw it referenced elsewhere as “–download human_genome bowtie2” and that worked.
So a note to whoever can update the page, I believe that command needs to read “human_genome” rather than just “human”
Thanks a lot, and cheers,