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?



IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.