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Question: Yeast genome reference in Bowtie2
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gravatar for Yue
3.4 years ago by
Yue • 0
United States
Yue • 0 wrote:

I am trying to do some data analysis of my Chip Seq data in yeast. And I stuck at the alignment step because I cannot find any yeast genome reference in Bowtie2. I am wondering whether you guys can help me to fix this, or if have any other suggestions.

Thank you!
alignment bowtie • 1.5k views
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modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by Yue • 0
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gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use a yeast genome as a Custom Reference Genome. UCSC is one source. Genomes at this site are in the downloads area inside directories named "Full data set": http://hgdownload.soe.ucsc.edu/downloads.html#yeast

Download the target file using UCSC's instructions, uncompress if tar.gz, then load into Galaxy via the upload tool. The 2bit version is also an option if you have the UCSC source tools on your computer (convert using twoBitToFasta). However, in most cases, the file you want will be named something like "chromFa.tar.gz". If the genome is split by chromosome, merge these together on your computer before loading into Galaxy with line-command tools, or merge in Galaxy after loading each with the tool "Concatenate".

Best, Jen, Galaxy team
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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