Just a word of warning to everyone. I have recently been trying to map S.Cerevisiae sequencing reads to a reference genome. The pre built index supplied by bowtie is built on the CYGD assembly and not the commonly used SGD assembly (strain S288C). I'm unsure if CYGD use a different strain or an older assembly but I have noticed differences (mainly SNPs) in the sequence files.
Shaun Webb
Hi Shaun,
The sacCer2 genome is annotated as SGD/S288C June 2008 at UCSC. Is this not what you are expecting/finding when doing your analysis in Galaxy NGS Mapping with sacCer2?
Thanks for helping us to understand!
Jen Galaxy Team
On 8/17/10 5:55 AM, SHAUN WEBB wrote:
Just a word of warning to everyone. I have recently been trying to map S.Cerevisiae sequencing reads to a reference genome. The pre built index supplied by bowtie is built on the CYGD assembly and not the commonly used SGD assembly (strain S288C). I'm unsure if CYGD use a different strain or an older assembly but I have noticed differences (mainly SNPs) in the sequence files.
Shaun Webb
I have been using my own instance of Galaxy and installed the pre-built index supplied on the Bowtie website. I have recently realised that the index supplied by the bowtie developers is different from the downloadable sequence at SGD. Although not directly linked to Galaxy I thought I would make everyone aware, hope that is a little clearer. I have also been in touch with the developers of Bowtie.
Shaun
Quoting Jennifer Jackson jen@bx.psu.edu:
Hi Shaun,
The sacCer2 genome is annotated as SGD/S288C June 2008 at UCSC. Is this not what you are expecting/finding when doing your analysis in Galaxy NGS Mapping with sacCer2?
Thanks for helping us to understand!
Jen Galaxy Team
On 8/17/10 5:55 AM, SHAUN WEBB wrote:
Just a word of warning to everyone. I have recently been trying to map S.Cerevisiae sequencing reads to a reference genome. The pre built index supplied by bowtie is built on the CYGD assembly and not the commonly used SGD assembly (strain S288C). I'm unsure if CYGD use a different strain or an older assembly but I have noticed differences (mainly SNPs) in the sequence files.
Shaun Webb
-- Jennifer Jackson http://usegalaxy.org
Thanks Shaun for explaining the different indexes/sources!
Jen
On 8/17/10 7:42 AM, SHAUN WEBB wrote:
I have been using my own instance of Galaxy and installed the pre-built index supplied on the Bowtie website. I have recently realised that the index supplied by the bowtie developers is different from the downloadable sequence at SGD. Although not directly linked to Galaxy I thought I would make everyone aware, hope that is a little clearer. I have also been in touch with the developers of Bowtie.
Shaun
Quoting Jennifer Jackson jen@bx.psu.edu:
Hi Shaun,
The sacCer2 genome is annotated as SGD/S288C June 2008 at UCSC. Is this not what you are expecting/finding when doing your analysis in Galaxy NGS Mapping with sacCer2?
Thanks for helping us to understand!
Jen Galaxy Team
On 8/17/10 5:55 AM, SHAUN WEBB wrote:
Just a word of warning to everyone. I have recently been trying to map S.Cerevisiae sequencing reads to a reference genome. The pre built index supplied by bowtie is built on the CYGD assembly and not the commonly used SGD assembly (strain S288C). I'm unsure if CYGD use a different strain or an older assembly but I have noticed differences (mainly SNPs) in the sequence files.
Shaun Webb
-- Jennifer Jackson http://usegalaxy.org
galaxy-dev@lists.galaxyproject.org
-
Jennifer Jackson -
SHAUN WEBB