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Question: Saccharomyces cerevisiae reference genome for TopHat,Bowtie
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gravatar for sv112
3.5 years ago by
sv112 • 10
United States
sv112 • 10 wrote:

Hi,

I am new to Galaxy, and for my first project I wish to analyze some sequences we recently obtained from an RNA-Seq experiment. I am stuck at the step of using TopHat/Bowtie for aligning my FASTQ files to a S.cerevisiae reference genome (preferably, S288C). The problem is that I don't see any S.cerevisiae reference genome from the list of built-in reference genomes. This is confusing, because Galaxy clearly has this sequence on its server (the genome option appears in the Get Data-->Upload file menu at the bottom right-hand corner, for example). Could you comment on this?

Anyway, I am currently trying to use the alternate option of manually uploading a reference genome to my history and using that as a reference for my analyses but even this isn't nearly as straightforward as I thought, probably because I have a Windows machine. Is there a source from where I can download an annotated S288C genome as a FASTA file as a single file?  I downloaded  S288C_reference_genome_R64-2-1_20150113.tgz but I only see Chromosome 1 in this file.

Thanks!

Sri

 
rna-seq tophat bowtie galaxy • 1.3k views
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modified 3.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.5 years ago by sv112 • 10
1
gravatar for Jennifer Hillman Jackson
3.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This genome is pending addition to this tool. The genome is included in other tools, but that does not have a relationship to the content of the list of builds (genomes) on the Upload or Edit Attributes forms. Only genomes listed per tool are indexed for that tool. And a genome not indexed for any is either not incorporated on purpose or is pending release.

BUT - the best news is that you don't need to wait for us, especially with such as easy genome to locate, load into Galaxy, and use a a Custom Reference Genome. The UCSC Genome browser is a great source for many common genomes. THe genome "sacCer3" is mostly likely what you are looking for, but a few releases exist there. 

Best, Jen, Galaxy team
ADD COMMENT • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k
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