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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___________________________________________________________
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:
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