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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
From: Aleks Schein <al...@mb.au.dk>
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] SAM to bigbed
Message-ID: <20110613184245.14175jqs5ml9m...@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
From: Jennifer Jackson <j...@bx.psu.edu>
To: Aleks Schein <al...@mb.au.dk>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] SAM to bigbed
Message-ID: <4df642c8.3070...@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,
>
> Aleks
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
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>
> http://lists.bx.psu.edu/

-- 
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/


------------------------------

Message: 3
Date: Mon, 13 Jun 2011 13:34:11 -0500
From: John David Osborne <ozb...@uab.edu>
To: "galaxy-u...@bx.psu.edu" <galaxy-u...@bx.psu.edu>
Subject: [galaxy-user] GenBank Submission - How to Generate Fasta (not
        fastq) files
Message-ID:
        <27f664987feadb4ea29031f58bc42b3e02144...@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.
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