-----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of galaxy-user-request@lists.bx.psu.edu Sent: Tuesday, June 14, 2011 9:00 AM To: galaxy-user@lists.bx.psu.edu Subject: galaxy-user Digest, Vol 60, Issue 14
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Today's Topics:
1. SAM to bigbed (Aleks Schein) 2. Re: SAM to bigbed (Jennifer Jackson) 3. GenBank Submission - How to Generate Fasta (not fastq) files (John David Osborne)
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Message: 1 Date: Mon, 13 Jun 2011 18:42:45 +0200 From: Aleks Schein aleks@mb.au.dk To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] SAM to bigbed Message-ID: 20110613184245.14175jqs5ml9mqrp@webmail.nfit.au.dk Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed"
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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Message: 2 Date: Mon, 13 Jun 2011 10:03:04 -0700 From: Jennifer Jackson jen@bx.psu.edu To: Aleks Schein aleks@mb.au.dk Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] SAM to bigbed Message-ID: 4DF642C8.3070000@bx.psu.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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,
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