Bob Harris

The sample in v1.5 appears to limit insert lengths to [1000,3000] for bowtie but to [1300,2300] for mateAn. Is this is mistake, or is there a reason why I should use different limits for the same sequencing run? For example, in my data I estimate most of the inserts are in [100,1100] with a mode around 500. Is there some reason I should tighten up that interval for mateAn?

Page 10 of the MANUAL describes columns 1-8 of the .metassem file. However, after running the provided example (for version 1.5), the .metassem file has another 10 columns. Posting this so that other users will know. I have no illusion that a package that was last updated 4 years ago is actively being supported.