Dear UCSC team members, I love to use the UCSC genome browser and all your tools. I think you do wonderful job helping the genome community. Recently I used the liftOver utility to take tophat bed file from hg18 coordinates to hg19 coordinates. After comparing the two files, I noticed that the hg19 bed file doesn't have the colour field in proper format and also there are some additional "," at the ends of fields 11,12.
For example: The hg18 bed file (input for liftOver): track name=junctions description="TopHat junctions" chr20 199843 204678 JUNC00000001 5 - 199843 204678 255,0,0 2 65,70 0,4765 chr20 205740 205898 JUNC00000002 3 - 205740 205898 255,0,0 2 46,32 0,126 chr20 205967 207017 JUNC00000003 5 - 205967 207017 255,0,0 2 57,47 0,1003 chr20 207905 212646 JUNC00000004 2 - 207905 212646 255,0,0 2 66,43 0,4698 chr20 212675 218928 JUNC00000005 1 - 212675 218928 255,0,0 2 47,29 0,6224 chr20 218249 218940 JUNC00000006 2 - 218249 218940 255,0,0 2 68,41 0,650 chr20 251166 276805 JUNC00000007 3 - 251166 276805 255,0,0 2 43,62 0,25577 chr20 277937 278346 JUNC00000008 10 + 277937 278346 255,0,0 2 70,65 0,344 chr20 278411 281899 JUNC00000009 3 + 278411 281899 255,0,0 2 65,46 0,3442 The hg19 bed file (output from liftOver): chr20 251843 256678 JUNC00000001 5 - 251843 256678 16711680 2 65,70, 0,4765, chr20 257740 257898 JUNC00000002 3 - 257740 257898 16711680 2 46,32, 0,126, chr20 257967 259017 JUNC00000003 5 - 257967 259017 16711680 2 57,47, 0,1003, chr20 259905 264646 JUNC00000004 2 - 259905 264646 16711680 2 66,43, 0,4698, chr20 264675 270928 JUNC00000005 1 - 264675 270928 16711680 2 47,29, 0,6224, chr20 270249 270940 JUNC00000006 2 - 270249 270940 16711680 2 68,41, 0,650, chr20 303166 328805 JUNC00000007 3 - 303166 328805 16711680 2 43,62, 0,25577, chr20 329937 330346 JUNC00000008 10 + 329937 330346 16711680 2 70,65, 0,344, chr20 330411 333899 JUNC00000009 3 + 330411 333899 16711680 2 65,46, 0,3442, I will be thankful if you can help me solve this issue. Thanks in advance, Oz Solomon Cancer Research Center, Sheba hospital, Israel _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
