Hi René, See answers below on what tracks to start with and then you can use the table browser to extract the information you want:
1. all known ncRNAs excluding tRNAs and rRNAs Please take a look at the RNA Genes Track (http://genome/cgi-bin/hgTrackUi?db=hg18&c=chrX&g=rnaGene<http://genome/cgi-bin/hgTrackUi?db=hg18&c=chrX&g=rnaGene> ). In the table browser you can filter out tRNAs and rRNAs by their names. To exclude the tRNA and rRNA genes in that track, go to the Table Browser and select the 'rnaGene' table, then create a filter on that table so that "type doesn't match tRNA rRNA" Please note the space between "tRNA rRNA " 2. tRNAs Please take a look at the tRNA track on hg19: http://genome/cgi-bin/hgTrackUi?db=hg19&c=chr2&g=tRNAs If you want to use hg18 and use the RNA Genes Track, here is a previously answered mailing list question with regards to tRNAs: https://lists.soe.ucsc.edu/pipermail/genome/2007-October/014924.html 3. rRNAs Please take a look at the RNA Genes Track on hg18: http://genome/cgi-bin/hgTrackUi?db=hg18&c=chrX&g=rnaGene To see a list of only the rRNA genes in that track, go to the Table Browser and select the 'rnaGene' table, then create a filter on that table so that "type does match rRNA" 4. 3' and 5' UTRs of all coding RNAs: In the table browser, do the following settings as you stated before: * clade: Mammal*>* genome: Human*>* assembly: hg19*>* group: Genes and Gene Prediction Tracks*>* track: RefSeqGenes*>* table: refGene*>* region: genome*>* Then you will need to use the filter setting and this refSeq key ( http://www.ncbi.nlm.nih.gov/RefSeq/key.html) to decide which identifiers you want or don't want. Please note that you can filter multiple queries by separating them with a space like this " NR_* NM_* " To get the sequences in the table browser you will need to select: output format: sequence Hopefully this will get you started. If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: René Böttcher <[email protected]> Date: Fri, Apr 6, 2012 at 1:36 AM Subject: [Genome] extract ncRNA sequence data via table browser To: [email protected] 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 This track 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
