Thanks for the responses It appears these programs require some background in Python or R. Is there a less code-intensive way to manipulate a sam or bam into a format viewable in Excel? Does Galaxy provide a tool for this?

If it simply is a matter of learning code, so be it.

On Fri, Oct 11, 2013 at 3:20 PM, Gabriel Calvin <gac4223@gmail.com> wrote:

The organism is fruit fly. The piRNA reference sequence was obtained from http://www.fruitfly.org/p_disrupt/TE.html as FASTA.FORMAT.v9.4.1.

I will check out those programs.

Gabriel