I am in need of your collective bioinformatic brains.

Here is my situation:

I have data sets of small RNAs from Solexa sequencing. I'm wanting to calculate the expressions of these small RNAs, but having some issues. To calculate expressions I used SAM output from Bowtie and used Cufflinks to calculate the expressions. The expressions calculated people in my lab are having concerns about. The small RNAs should be <35bps, but the calculations from Cufflinks involve regions that are much larger than 35bps. People in my lab wish to calculate expression for only the regions <35bps and I can only think of doing this by doing counts. Is Cufflinks an inappropriate expression calculation tool for small RNAs (miRNAs, siRNAs, etc.)? Or is there another program I could used to achieve this? I think Cufflinks is calculating the expressions correctly, but I thought I would reach out to all of you and ask.

Thanks in advance.

-Brandon

Here is my situation:

I have data sets of small RNAs from Solexa sequencing. I'm wanting to calculate the expressions of these small RNAs, but having some issues. To calculate expressions I used SAM output from Bowtie and used Cufflinks to calculate the expressions. The expressions calculated people in my lab are having concerns about. The small RNAs should be <35bps, but the calculations from Cufflinks involve regions that are much larger than 35bps. People in my lab wish to calculate expression for only the regions <35bps and I can only think of doing this by doing counts. Is Cufflinks an inappropriate expression calculation tool for small RNAs (miRNAs, siRNAs, etc.)? Or is there another program I could used to achieve this? I think Cufflinks is calculating the expressions correctly, but I thought I would reach out to all of you and ask.

Thanks in advance.

-Brandon

## Comment