Question: Where to find Drosophila melanogaster de novo transcript assembly data?
gravatar for Peter vH
22 months ago by
Peter vH130
Peter vH130 wrote:

I am studying de novo (non-model) genome annotation and would like to use a well characterised organism to test some of my methods. To this end I am looking for an assembled de novo transcriptome dataset for Drosophila melanogaster, preferably assembled from short read data. Does anyone know where to find such a dataset? Thank you!

ADD COMMENTlink modified 15 months ago by jaudall0 • written 22 months ago by Peter vH130

It would still be useful ... coincidently I'm looking for it too to test a genome annotation pipeline.

ADD REPLYlink written 15 months ago by jaudall0
gravatar for Joseph Hughes
22 months ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

In this paper, you can find a list of SRA accessions for Drosophila short reads. They have also provided the statisitcs for different de-novo assemblers: Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. Unfortunately, they do not seem to provide the assembled transcripts. I imagine that for D. melanogaster it is probably rare that researchers would be doing de-novo transcript assembly as there is a very good genome to assemble to.

ADD COMMENTlink written 22 months ago by Joseph Hughes2.7k
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