I was recently pointed to your website to analyse my NGS data, my primary interest is in mapping small RNA reads to microRNA.

After following the tutorials (which are excellent)  I am able to upload and map with Bowtie by small RNA data set produced from the SOLID platform.

From this point I am completely lost with what to do next to obtain small RNA/microRNA mapped to the genome and a count of the tags etc as the RNA Analysis seams to be dedicated to transcript assembly and quantitation rather than microRNA from mirBase.

I have been also looking at the DARIO websever http://dario.bioinf.uni-leipzig.de/index.py for doing the mapping, but I need to convert my BOWTIE SAM output to either BED or BAM file format and remain under 60MB in size.

They suggest that the converting the mapping results to BED file be done with map2bed.pl (does Galaxy have a tool for this). 

For conversion of the mapping to BAM, I can use SAM to BAM with SAMTOOLS with header file intact as this is required for DARIO calculations.

This also seems a problem as I dont think I have the header information intact.

Any help or suggestions would be appreciated.