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(a)bx.psu.edu&gt;: > 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