Hi Shayne

For the SAM to BED conversion, you can use the tool: "NGS: SAM Tools"->"Convert SAM to interval"


Regards, Hans


On 06/20/2011 07:10 AM, Shayne Bellingham wrote:
Dear Galaxy Team,

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.

Shayne A. Bellingham

Department of Biochemistry and Molecular Biology
Bio21 Molecular Science and Biotechnology Institute
The University of Melbourne
30 Flemington Road
Parkville VICTORIA 3010
AUSTRALIA




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