Good Morning Oz: To preserve the structure of the TopHat output format, use the option: -bedPlus=8 on your liftOver command line.
Your input example: 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 Becomes: 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 liftOver -bedPlus=8 yourInput.bed hg18ToHg19.over.chain.gz hg19Output.bed unmapped.txt --Hiram oz solomon wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
