Hi Vinay, I apologize for the delayed response.
Yes, there is data that attempts to use RNA-seq alignments to quantify the expression level of known gene models. Please see the RPKM subtracks of the HudsonAlpha RNA-seq track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeHudsonalphaRnaSeq). There are also some attempts to build elements/clusters using the alignments. Please see the "Clusters" subtracks in the GIS PET Loc track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeGisPet). Unfortunately, there isn't any exhaustive annotation of these RNA-seq reads. The ENCODE analysis team is still in the process of analyzing all of the data. Please don't hesitate to contact the mail list again if you have any further questions. Thank you, Katrina Learned UCSC Genome Bioinformatics Group Mittal, Vinay K wrote, On 08/11/10 11:08: > Hi, > I have been trying to look more into the ENCODE RNA-seq data for human cell > lines. I tried to download data files from ENCODE DCC database but all I got > was alignments (which can be viewed in the UCSC browser) and raw sequencing > reads. I was wondering if there is any data on the > characterization/annotation of each RNA-seq read for the ENCODE project. > > Thanks. > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
