Sample SAM file for tutorial

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Sample SAM file for tutorial

Scott Cain
Hello,

Does anyone happen to have a SAM file that would be useable with the  
"volvox" tutiorial?

Thanks,
Scott


Sent from my iPhone

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Re: Sample SAM file for tutorial

Fields, Christopher J
One could probably create a simple one using a small set from wgsim against the mRNA for the genes in the volvox set (I think this will even generate paired-end data if you need it).

chris

On Oct 23, 2011, at 6:17 PM, Scott Cain wrote:

> Hello,
>
> Does anyone happen to have a SAM file that would be useable with the  
> "volvox" tutiorial?
>
> Thanks,
> Scott
>
>
> Sent from my iPhone
>
> ------------------------------------------------------------------------------
> The demand for IT networking professionals continues to grow, and the
> demand for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn
> about Cisco certifications, training, and career opportunities.
> http://p.sf.net/sfu/cisco-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
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http://p.sf.net/sfu/cisco-dev2dev
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Re: Sample SAM file for tutorial

Scott Cain
Hi Chris,

Yes, excellent, I knew there was a tool that was something like that, I just didn't know what it was.  I downloaded and compiled it, used the "volvox" fasta file and create paired read fastq files, then loaded them into Galaxy and ran bowtie on them to produce a SAM file.  Piece of cake :-)

Scott


On Sun, Oct 23, 2011 at 10:31 PM, Fields, Christopher J <[hidden email]> wrote:
One could probably create a simple one using a small set from wgsim against the mRNA for the genes in the volvox set (I think this will even generate paired-end data if you need it).

chris

On Oct 23, 2011, at 6:17 PM, Scott Cain wrote:

> Hello,
>
> Does anyone happen to have a SAM file that would be useable with the
> "volvox" tutiorial?
>
> Thanks,
> Scott
>
>
> Sent from my iPhone
>
> ------------------------------------------------------------------------------
> The demand for IT networking professionals continues to grow, and the
> demand for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn
> about Cisco certifications, training, and career opportunities.
> http://p.sf.net/sfu/cisco-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
about Cisco certifications, training, and career opportunities.
http://p.sf.net/sfu/cisco-dev2dev
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Re: Sample SAM file for tutorial

Fields, Christopher J
Actually, I would be surprised if wgsim isn't already wrapped in galaxy (maybe not the PSU one); we're planning on setting that one up locally for a number of researchers.

Anyway, glad to hear that worked.

chris


On Oct 24, 2011, at 8:28 AM, Scott Cain wrote:

> Hi Chris,
>
> Yes, excellent, I knew there was a tool that was something like that, I just didn't know what it was.  I downloaded and compiled it, used the "volvox" fasta file and create paired read fastq files, then loaded them into Galaxy and ran bowtie on them to produce a SAM file.  Piece of cake :-)
>
> Scott
>
>
> On Sun, Oct 23, 2011 at 10:31 PM, Fields, Christopher J <[hidden email]> wrote:
> One could probably create a simple one using a small set from wgsim against the mRNA for the genes in the volvox set (I think this will even generate paired-end data if you need it).
>
> chris
>
> On Oct 23, 2011, at 6:17 PM, Scott Cain wrote:
>
> > Hello,
> >
> > Does anyone happen to have a SAM file that would be useable with the
> > "volvox" tutiorial?
> >
> > Thanks,
> > Scott
> >
> >
> > Sent from my iPhone
> >
> > ------------------------------------------------------------------------------
> > The demand for IT networking professionals continues to grow, and the
> > demand for specialized networking skills is growing even more rapidly.
> > Take a complimentary Learning@Cisco Self-Assessment and learn
> > about Cisco certifications, training, and career opportunities.
> > http://p.sf.net/sfu/cisco-dev2dev
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research


------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
about Cisco certifications, training, and career opportunities.
http://p.sf.net/sfu/cisco-dev2dev
_______________________________________________
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