Test if Bowtie2 --very-sensitive options are working

Question

[anthonyc]

Hi All, Does anyone know of a way to test if the options for Bowtie2 are working? Specifically, I am wondering if there is a way to test if the --very-sensitive option is working. It seems to not produce any difference on a couple of data sets. Is there a standard data set that could be run with and without the option to see if the parameters are being used?

Thanks!

[Devon Ryan]

I've never seen a test dataset for that, which is too bad actually. In my experience the difference due to --very-sensitive is quite minor (this isn't the case for local alignment).