construct annotation files

[FLYINGDOLPHIN]

Hi all,

I am interested in checking the non-coding rna(for example, transposons) expression levels.However, there is no annotation file (GTF for example). Does anyone know how to make the file in order to be used in tophat workflow?

Thanks a lot!

Best,
F

[Wallysb01]

Is this for some newly sequenced species or something without any official genome annotation? Because if you need to create that, its a lot of work.

[Eveleee]

Transcriptom annotation

Dear all, I have probably no right to start new thread. So sorry, for the wrong placing.
We have transcriptom data, Illumina Hiseq assembled, from species complex of Cobitis fish. Unfortunatelly, there is no reference seq. The most relative species is Danio rerio.
We need a good annotation for further comparisions of thranscriptoms from different species. We would like to compare the transcription activity in different species.
Some recomends PASA or MAKER. Maker is used for small genoms, pasa for spliced seq. I thing in our case when the size of the genom is 13 MB, PASA will be bether.
One colegue recomended me to use RAST as well, but it seems to be for procaryots.
Do you thing, that the tools use preferently searching in databases for procaryotics? What is the algorithm?
Which one would you use in this case?
Which toll is the best to use for visualisation the annotated data?
Is the output from GMOD unappropriate to submit the seq in GO?
I know RAST comunicate with GMOD.
Which annotators would you recomend me?
Thank you