You can also try miRDeep_star. It identifies know miRs and discovers
possible new miRs. There is a java gui and a command line option. However
you have to get your genome indexed with a script they provide. I used
Deseq for the known miRs as well.

Luciano

Sent from my HTC One.
On Oct 11, 2013 12:19 PM, "Hoang, Thanh" <hoan...@miamioh.edu> wrote:

> 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
> Thanh
>
>
> On Fri, Oct 11, 2013 at 12:51 PM, Gabriel Calvin <gac4...@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?
>>
>> Thanks!
>>
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>
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