Hello,
I need the gene description file for rice (japonica and indica both) for my RNASeq annotation work. 1. can anyone direct me to the source? 2. What is the file format for such a file?
http://plants.ensembl.org/index.html has multiple rice annotations, presumably different species or strains or whatever that is called in plant biology. The file you are looking for, if I understand correctly, is a .gtf or .gff file.
Illumina iGenomes has a sequence/index/annotation bundle available for japonica (not for indica though). Going this route saves issues with mismatches on names, annotation etc.
As noted by @Wouter: Ensembl plant has Indica and Japonica sequences (FASTA files) and annotations (GFF3) files available. You will need to build aligner indexes yourself.
If you have already done alignments with some reference then it would be best to find a corresponding annotation file that goes with that genome build or start over with one of the resources above.
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Thanks for your answers. I did used these files for my alignment. I am using gfold and used the corresponding .gtf file for annotation but since the gfold manual mentioned the gene description file seperatly, I got confused.
Well, I used the japonica.gtf file in gfold, still the gene description column is empty (N/A). According to the manual, I used -d japonica.gft in my command line, but no result in that column. Can u help here or Should I stat a new question?
GFOLD manual describes the format that is expected for the GTF file. It may just be a matter of reformatting your file to fit that expectation.
ok, i get it. But how can I reformat the downloaded .gtf file?
Not sure what your file looks like currently but some awk (or failing that a scripting solution) should be able to reformat the file.
Thanks genomax2 I'll try and if not successful, will come back here.