Question: Sam To Bigbed
gravatar for Aleks Schein
7.5 years ago by
Aleks Schein60
Aleks Schein60 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
samtools bam • 803 views
ADD COMMENTlink modified 7.5 years ago by Jennifer Hillman Jackson25k • written 7.5 years ago by Aleks Schein60
gravatar for Jennifer Hillman Jackson
7.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson
ADD COMMENTlink written 7.5 years ago by Jennifer Hillman Jackson25k
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