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Question: Schizosaccharomyces pombe on Tophat
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gravatar for sina.wittmann
2.9 years ago by
sina.wittmann • 0
sina.wittmann • 0 wrote:

I was trying to use Tophat for my RNA-Seq data derived from S. pombe. However, S. pombe was not part of the drop down menu. It is included in bowtie though. Is it possible to add it to Tophat as well?

Thanks.
tophat custom-genome • 682 views
ADD COMMENT • link •
modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by sina.wittmann • 0
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I just added the Schizosaccharomyces_pombe_1.1, sacCer2, sacCer3 genomes to the test server at https://test.galaxyproject.org/ for the Bowtie2, Tophat(2), and HISAT2 mapping tools.

We are using a new method to add indexes. If you would like to help test these, please give the new indexes a try. Should errors any occur or simply unexpected results, a bug report/shared history link from the test instance would be welcomed.

We'll also test more here and promote to the Main server at http://usegalaxy.org as soon as possible, along with several other genomes that are in our queue.

If you need to use the genome on the Main server immediately, the option to use a Custom reference genome is still an option (this is true for any reference genome/transcriptome). UCSC is often the best source for the fasta version of a genome, if the genome is supported by them, as many ancillary files commonly used with RNA-seq tools will have the same sequence identifiers (example: reference annotation from iGenomes).

https://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks and have a great weekend, Jen, Galaxy team
ADD COMMENT • link modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

Also added to BWA/BWA-MEM. There is a duplicate for sacCer3 - our team will resolve that next week.

If anyone is interested in trying the indexes for that tool, our team is also interested the same type of feedback about job success/failure.

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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