Question: Where To Download Annotated Transcripts Of Schizosaccharomyces Pombe?
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gravatar for Shaojiang Cai
7.2 years ago by
Shaojiang Cai100
Singapore
Shaojiang Cai100 wrote:

Hi, all,

We have two sets of contigs assembled by Trinity and Oases (on S.pombe). We would like to compare the performance of them in terms of full length transcripts. I understand that a transcriptome depends on the condition when it was sequenced. But is there some annotated transcripts are relatively "complete"? By "complete" I mean it captures splicing forms of the genes.

I have found Pombase, which provides genome and genes but no transcripts. Also there is a Science paper from Broad Institute, which provides transcripts in FASTA format (http://www.broadinstitute.org/annotation/genome/schizosaccharomyces_group/MultiHome.html). Is this dataset good for my application? Or any other one is better?

Thanks.

transcriptome download • 1.9k views
ADD COMMENTlink modified 7.2 years ago by Josh Herr5.7k • written 7.2 years ago by Shaojiang Cai100
1
gravatar for Josh Herr
7.2 years ago by
Josh Herr5.7k
University of Nebraska
Josh Herr5.7k wrote:

When it comes to Schizosaccharomyces I think the best you are going to get (as far as splicing forms, etc.) is the Broad database. You can download the data here. The transcripts are listed as "transcripts.fasta" and the annotation file is the "transcripts.gtf" file.

I'm not aware of any other transcriptome database information other than what you have mentioned, so I think your only option is to sequence your own transcriptome using your strain and culture conditions.

ADD COMMENTlink written 7.2 years ago by Josh Herr5.7k
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