Hello, It is possible to go from SAM/BAM to BED, but not the reverse. SAM/BAM files contain the actual sequence data associated with the original aligned read. BED files only have the reference genome location of the alignment (no read "sequence"). It is possible to extract genomic sequence based on BED coordinates, but the resulting sequence would not necessarily be the same sequence as in the original aligned read (any variation would be lost). BED is very similar to Interval format, so Interval tools also work with BED format. A BED file is basically a 3-12 column, tab delimited file, so tools that work with Tabular data are also appropriate for BED file. Note that you may need to change the datatype to be interval or tab for certain tools to recognize a BED file as an input. Hopefully this helps, Jen Galaxy team On 9/22/11 2:55 PM, shamsher jagat wrote:
Is it possible to use some tool in Galaxy to convert BED file to Bam/ sam file. In other word do we have Bed tools or other option in Galaxy
Thanks
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support