Hi Aleks,

There is no function in Galaxy for this in one step, but there are other options:


1) only convert to BAM and view at UCSC that way, if visualization is your goal. This preserves the primary sequence information in the file so that it can be viewed/used in downstream analysis.

2) use "Generate Pileup" then "Pileup-to-Interval". Interval can be changed to BED using the pencil icon (you may need to arrange column order first to meet spec, as BED columns must be in a specific order, as defined on any of the tools involving BED files). The resulting BED file can then be condensed by "BED-to-bigBed". This loses the primary sequence information - only coordinates are retained - may or may not be desirable.

Hopefully this helps,

Jen
Galaxy team

On 6/13/11 9:42 AM, Aleks Schein wrote:
Hi,
Is it possible to generate a bigbed or bigwig file from SAM (or BAM)
file using Galaxy? It looks like there is such option in the full
version of SAMTools, but I have no appropriate machine to run SAMTools.

Thanks,

Aleks
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