Hi.
I'm trying to retrieve transcript sequenceses from transcripts IDs. I need the same transcript version from the one used in the experiment that i'm considering, in which version is missing.
I know from the experiment description that raw reads were mapped to hg19 transcriptome, which was aggregated from UCSC RefSeq and Genecode v12 databases.
I've tried to use GTF file from hg19, but versions don't match. I'm working on a large dataset, so i'll need a easy and direct way to determinate the right versions.
Thank you!
Adelaide
Why do you not want to use the latest version of the RefSeq transcripts? There may be very minor changes but in any case the latest version reflects the best information available at the present.
Because for each transcript i have a string of scores, each score referred to a single nucleotide, than it's important for me to know the correct sequence. Morover different versions change in lenght, the positional score information would be unuseful.