Dear UCSC, I am fairly new to using UCSC and hence I am overwhelmed by the possibilities offered. So to speed up my work and get the data I need, I wanted to make use of your experiences and learn more at the same time. What I intend to do is separately download the sequences of:
1. all known ncRNAs excluding tRNAs and rRNAs 2. tRNAs 3. rRNAs 3. 3' and 5' UTRs of all coding RNAs So far, I've been looking at previous postings in the list to get some idea on how to proceed and find the right tables to look in. Nevertheless, the results I got for my ncRNAs were confusing. What I did was follow the description given here: https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025470.html Summed up that means: *> clade: Mammal*>* genome: Human*>* assembly: hg19*>* group: Genes and Gene Prediction Tracks*>* track: RefSeqGenes*>* table: refGene*>* region: genome*>* filter: click 'create' then in the 'name DOES match' field type: NR_** This results in 6,928 items being found. However, when I download the sequences, I only get 6,109 different items (Hg19, similar issue for Hg18 but with different counts). So I am a little confused on what happened to the rest of the sequences. Moreover, if I understand the RefSeq identifiers correctly, tRNAs and rRNAs are included in this list as well. So how can I download these separately? Many thanks in advance, René _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
