I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I 
have aligned the reads using Bowtie, but it appears that Cufflinks gives an 
error when run on the Bowtie alignments (This might have something to do with 
Bowtie's BAM file not being sorted). I know that Tophat alignments work well 
with Cufflinks, but I'm not sure if it would be possible to use Tophat for my 
data since miRNA don't have splice junctions. I've tried without success to 
parameterize Tophat to completely avoid assigning splice junctions (by setting 
the max intron length to 1).  Is there a way I can get the Bowtie alignment to 
work with Cufflinks on Galaxy? Or perhaps there's a way I can parametrize 
Tophat as to get no splice junctions?



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