Hi Gabriel,
  I believe you can do it with galaxy. I never used it for miRNA analysis because most of the miRNAs of the organism that I work with are not annotated on its genome. You will need the total number of reads that uniquely map to each mature miRNA. What I have notice is that the guide and passenger strand most of the time have huge differences in expression. To get that your annotation file (gtf or gff) would have to have each strand, its okay if you don't have it. Probably you can use HTseq. It is available on the Galaxy tool shed. You can also use it directly at http://galaxy.nbic.nl/ (it is NGS:RNA Analysis). You can also run it on your computer http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
  After you get the counts you can use Deseq to calculate differential expression. See if you can get the counts first. I never used the Galaxy Deseq wrapper, but they have it on the tool shed too. You can install R and the Deseq package on your computer. You might install RStudio as well. I can send you the code I used to do my analysis with comments if you decide to give it a try.


On Mon, Oct 14, 2013 at 1:13 PM, Gabriel Calvin <gac4223@gmail.com> wrote:
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.


Luciano Cosme

PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
979 845 1885