Hello Teja,

If you have a fasta file of sequences, you can map them to a reference genome to obtain a SAM file (which you could then compress into BAM). See the tool section "NGS Toolbox".


BLAST is an alignment tool and additional parsing/analysis tools would be needed in order to identify SNPs. If you do your analysis this way, and SNPs are called outside of Galaxy using your own methods, the final output could be converted into a format such as BED. Then Galaxy could be used to perform analysis vs public SNP databases.

To locate the SNP tools available Galaxy, in the left pane of the UI, choose "Options -> Show Search Tool" and enter the keyword "SNP".

Please let us know if you would like help with any of the tools,

Best,

Jen
Galaxy team

On 5/13/11 2:53 PM, sukeerthi teja Rallapalli wrote:

Hi,

Is it possible to convert a fasta file to sam/bam format using galaxy. ?

OR

Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast)

Thank you
Teja





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