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

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