Hi,
I'd like to report a strange bug: when making custom track/bed file of the knownGene exons using Table tool for the whole genome I get a number of exons that are not in actual knownGene track. For example more than 100 extra exons are listed for region chr15:22787248-22813789 (hg18). That region has only 3 ucsc genes overlapping: chr15 22751162 22795318 uc001ywz.1 0 + 22774020 22776299 0 6 140,96,139,126,138,109, 0,7191,22855,23270,25024,44047, chr15 22751162 22795318 uc001yxa.1 0 + 22751162 22751162 0 7 140,96,151,107,138,663,109, 0,7191,13009,24613,25024,26852,44047, chr15 22778014 22817591 uc001yxc.2 0 + 22778014 22778014 0 9 663,121,109,130,356,164,122,42,762,0,16591,17195,18470,19583,20950,37252 ,38053,38815, and correspondingly 22 exons. This could be seen when making exon track for the region only. However when creating such track for the whole genome (hg18) the same region on chr15 has 139 exons, listing 119 extra exons, Below are just a few of those (let me know if you want me to post whole list): chr15 22758353 22758449 uc001ywp.1_exon_4_0_chr15_22758354_f 0 + chr15 22764171 22764322 uc001ywy.1_exon_2_0_chr15_22764172_f 0 + chr15 22765034 22765069 uc001ywu.1_exon_3_0_chr15_22765035_f 0 + chr15 22770527 22770696 uc001ywx.1_exon_3_0_chr15_22770528_f 0 + chr15 22770550 22770696 uc001ywp.1_exon_6_0_chr15_22770551_f 0 + chr15 22770881 22771197 uc001ywv.1_exon_5_0_chr15_22770882_f 0 + chr15 22771597 22771749 uc001ywy.1_exon_4_0_chr15_22771598_f 0 + chr15 22772544 22772656 uc001ywp.1_exon_8_0_chr15_22772545_f 0 + chr15 22772544 22772656 uc001ywy.1_exon_5_0_chr15_22772545_f 0 + chr15 22773116 22773269 uc001ywp.1_exon_9_0_chr15_22773117_f 0 + chr15 22774017 22774156 uc001ywy.1_exon_7_0_chr15_22774018_f 0 + chr15 22774432 22774558 uc001ywp.1_exon_11_0_chr15_22774433_f 0 + chr15 22774646 22774822 uc001ywp.1_exon_12_0_chr15_22774647_f 0 + chr15 22778233 22780030 uc001yxb.2_exon_0_0_chr15_22778234_f 0 + chr15 22781099 22784472 uc001yxd.2_exon_0_0_chr15_22781100_f 0 + Could you please check this? I haven't noticed similar problem for any other gene prediction tracks, only for known genes. Thanks! Irina Khrebtukova Illumina, Hayward CA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
