Hi Calvin,
I am analyzing miRNA differential expression from my small RNA sequencing data from mouse tissue using Bowtie > Htseq>Deseq.
I tried both whole mouse genome and hairpin miRNA( from miRbase) as reference sequences and annotation of all known miRNA (from miRbase). These worked for me.
Another option is that you can try mirDeep2 and Novoalign.
Anyway, what organism are you working with? Where u download the piRNA reference sequence?
Let me know what happens

On Fri, Oct 11, 2013 at 12:51 PM, Gabriel Calvin <gac4223@gmail.com> wrote:
Hi, I'm new to Galaxy and am trying to view several miRNA datasets as a differential expression. The pipeline I'm using is Bowtie for Illumina (paired-end run) > SAM-to-BAM > ? > xls. The references I used with Bowtie are a mature miRNA fasta and a piRNA fasta and the reads are 30nt in length.

So, my questions are: Is this the proper pipeline? How do I go about converting the BAM into a xls file viewable in Excel?


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