Where can I download the UCSC refFlat files, say, for Arabidopsis Thalina, in order to generate the transcript sequences?
It seems that UCSC does not provide support for Arabidopsis so we will have to prepare the file by ourselves (based on the NCBI release). Fortunately, you can download the package prepared by Hongkai Ji at Johns Hopkins at http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/download.htm, choose the Genome Database for TAIR8 and unzip it. You can find the genome sequences and the refFlat.txt file (in subdirectory “annotation”).
