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I'm working on an RNA-Seq project in Arabidopsis thaliana and am planning on using Erange. Of course I need to first build an expanded genome to align the reads against. The scripts supplied with Erange to extract flanking sequences around splice sites use the knownGene table data from the UCSC Genome site. Of course there is no Arabidopsis data at UCSC (due to their prejudice against the Plant Kingdom 
). Of course TAIR has a fantastic GFF3 with all the required data. Before I do the work to transform the GFF3 file to the knownGene format (because let's face facts, I'm lazy) I thought I would ask:
1) Does anyone have or know of an expanded genome for A. thaliana (TAIR8)?
--or--
2) Does anyone have or know of TAIR8 annotations in a knownGene format file?
--or--
3) Does anyone have or know of a script to convert annotations in a GFF3 file to a knownGene format file?
Much appreciation and good karma would be bestowed.
). Of course TAIR has a fantastic GFF3 with all the required data. Before I do the work to transform the GFF3 file to the knownGene format (because let's face facts, I'm lazy) I thought I would ask:1) Does anyone have or know of an expanded genome for A. thaliana (TAIR8)?
--or--
2) Does anyone have or know of TAIR8 annotations in a knownGene format file?
--or--
3) Does anyone have or know of a script to convert annotations in a GFF3 file to a knownGene format file?
Much appreciation and good karma would be bestowed.