Hi, I am trying to export a BED file containing the alignmens for all of the chicken ESTs/mRNAs that map to the human genome (assembly hg19). It looks as if this should be possible through the hg19 table browser when appropriate filters are applied, but I can¹t seem to find any valid literature discussing how this might be done. I did search your mailing list archives and discovered a thread from 2004 (see cut/paste below) that used the free-form query box and:
type = "EST" and (organism = 318 or organism = 7952 or organism = 6744) but type¹ doesn¹t appear to be a valid MySQL field for the latest release of the human genome assembly. I also attempted to retrieve alignments by uploading a list chicken ESTs (GenbankIDs) that I downloaded from the chicken genome assembly, but since a good number of these don¹t map to the human genome, I get an error message indicating that one or more identifier has no match in table xenoEST, field qName. The browser doesn¹t seem to want me to retrieve thost that do match. If I could somehow establish a set of chicken ESTs that do map to the human genome I¹d be home free, but alas I just can¹t figure out a way to derive this information. Not unexpectedly, my attempts to open ³all² XenoEsts in Excel (for the purposes of cross-referencing with my chicken EST list) don¹t work when the file is 1.2GB+! Can you help?? Regards, Pete Dr. Peter V. Lovell 503-418-2651 Dept. of Behavioral Neuroscience Oregon Health & Science Univ 3181 SW Sam Jackson Park Road L470 Portland, OR 97239-3098 https://lists.soe.ucsc.edu/pipermail/genome/2004-June/004823.html [Genome] table browser, filter hg16 data v. chicken ESTs _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
