Hi, I was wondering if it is normal and expected for the CCDS clusters to contain overlapping lists of known gene transcripts? For example:
mysql> select * from ccdsKgMap where geneId='uc001cry.3'; +-------------+------------+-------+------------+----------+---------------+ | ccdsId | geneId | chrom | chromStart | chromEnd | cdsSimilarity | +-------------+------------+-------+------------+----------+---------------+ | CCDS44138.1 | uc001cry.3 | chr1 | 50513685 | 50667540 | 0.983784 | | CCDS44140.1 | uc001cry.3 | chr1 | 50513685 | 50667540 | 0.983784 | | CCDS553.1 | uc001cry.3 | chr1 | 50513685 | 50667540 | 0.955381 | +-------------+------------+-------+------------+----------+---------------+ 3 rows in set (0.00 sec) According to this query, uc001cry.3 transcript belongs to three different CCDS clusters. My intuitive (and obviously incorrect) understanding of how CCDS is compiled would be that each CCDS entry maps to a unique set of knownGene transcripts. Is there a detailed description on how CCDS /KG relations are obtained? Thanks, Ivan -- Ivan Adzhubey, Ph.D. Instructor Genetics Division, Brigham & Women's Hospital Harvard Medical School HMS New Research Building, Room 0464C 77 Avenue Louis Pasteur Boston, MA 02115 tel.: (617) 525-4728 fax: (617) 525-4705 web: http://genetics.bwh.harvard.edu/genetics/members/Ivan_Adzhubey.html _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
