Hi Vishal, This previous mailing list question and answer may help you better understand how our chain/net tables are structured:
https://lists.soe.ucsc.edu/pipermail/genome/2006-August/011382.html As far as gaps of different lengths, you are correct - they are gaps between best matching chains. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/20/10 2:13 PM, Vishal R Patel wrote: > Hey, > > I see that the level for a chain in the netPanTro2 is different between the > genome browser and the table. > I am looking at the following region in hg18, chr1:465-19,890. > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:465-19,890 > > The alignment displayed with "netPanTro2" - "full" has gaps at level 1 which > are present in the table with a different level. > > Like this, > Level: 1 > Human position: chr1:10312-11327 > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=162777095&o=10311&t=11327&g=netPanTro2&i=2 > > But the same gap in the table hg18.netPanTro2 has level 2. > > #bin level tName tStart tEnd type human_size chimp_size > 585 1 chr1 464 19890 top 19426 19150 > 585 2 chr1 631 641 gap 10 0 > 585 2 chr1 663 685 gap 22 0 > 585 2 chr1 691 709 gap 18 0 > 585 2 chr1 759 780 gap 21 0 > 585 2 chr1 1249 1311 gap 62 0 > 585 3 chr1 1249 1311 nonSyn 62 62 > 585 2 chr1 10311 11327 gap 1016 0 > 585 3 chr1 10311 11327 nonSyn 1016 1723 > 585 4 chr1 10681 10997 gap 316 1023 > 585 5 chr1 10770 10969 nonSyn 199 219 > > Similarly the non-Syn region > *Type:* nonSyn > *Level:* 3 > *Human position:* chr1:10771-10969 > *Chimp position:* chr12:57677594-57677812 > But this record has level 5 in the table. Am I missing something here? > > My second question is, what do gaps of different length mean? I see in the > table for the same region there is a gap with human_size=316 and > chimp_size=1023 (level 4 in table and level 2 in browser). Are these > basically gaps between best matching chains? > > Thanks, > Vishal > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
