Indica rice genome and annotation files

Question

[chandimaa]

Hi I have tried several reference genome and annotation files but ran into errors with my RNASeq experiment. The Ensemble GeneID format is different, that makes it downstream analysis difficult. NCBI GenBank only has.gbff format NOT compatible with featurecounts? Please share a genome and annotation file combination that worked for you. Thank you Chandima

[dthorbur]

Please add more detail to your question. I am confused what the problem is. Why is Ensembl GeneID difficult? Personally, I find it easier than most GenBank IDs.

Which genome accession are you using? GCA_000004655.2 has all the files I would associate with an annotated genome. There are plenty of unannotated indica group genomes on NCBI, maybe you're using one of them.

Sometime groups don't upload the annotation data to NCBI, so you can sometimes find annotation data for specific genomes on other sites, but it's usually listed in the original publication.

[ChanderKant (CK) Chaudhary]

Yeah, add more description to the question. and I totally agree that Ensembl nomenclature is much easier than GenBank IDs.

[Picasa]

You can download both on ENSEMBL I guess.

Answer 1

[ChanderKant (CK) Chaudhary]

Ensembl plants should work. They have most of the rice annotation from RAP-DB (IRGSP-1.0). Additionaly, you can try RGAP.

Thank you.

Best,

CK