Question: Schizosaccharomyces pombe on Tophat
gravatar for sina.wittmann
2.9 years ago by
sina.wittmann0 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?


tophat custom-genome • 682 views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by sina.wittmann0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I just added the Schizosaccharomyces_pombe_1.1, sacCer2, sacCer3 genomes to the test server at 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 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).

Thanks and have a great weekend, Jen, Galaxy team

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k

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 REPLYlink written 2.9 years ago by Jennifer Hillman Jackson25k
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