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David Wang • 10 wrote:
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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)
Message: 1
Date: Mon, 13 Jun 2011 18:42:45 +0200
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
Message: 2
Date: Mon, 13 Jun 2011 10:03:04 -0700
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
SAMTools.
--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
Message: 3
Date: Mon, 13 Jun 2011 13:34:11 -0500
To: "galaxy-user@bx.psu.edu" <galaxy-user@bx.psu.edu>
Subject: [galaxy-user] GenBank Submission - How to Generate Fasta (not
fastq) files
Message-ID:
<27F664987FEADB4EA29031F58BC42B3E02144922@UABEXMBS5.ad.uab.edu>
Content-Type: text/plain; charset="iso-8859-1"
I still haven't found an easy solution to this problem and I am afraid
I'm going to have to write one my own - which makes little sense as I
bet this has been solved thousands of times!
Can anybody point me to a script/software to convert a samtools pileup
file into a fasta consensus file? It would be nice to set coverage
thresholds, etc... but I'll take anything I can work with.
The best google could do for me was this:
http://biostar.stackexchange.com/questions/1389/how-to-
generate-a-consen
sus-fasta-sequence-from-sam-tools-pileup
Not that helpful,
-John
P.S. If there is a better way of doing this (something other than
samtools) I'm all ears.
URL:
<http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20110613="" f579="" 0e82="" attachment-0001.html="">
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