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(a)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
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