Hi Sri, 1) The one base pair difference in the start positions is due to our 0-based coordinate system. Please see this FAQ for more information: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
2) The "strand:" information that you see on the item's details page is there in error; one of our engineers has removed it. Sorry for the confusion and thank you for bringing it to our attention! The 'strand' column in the genomicSuperDups table is represented in the item details by "Other Position Relative Orientation:." The items in this track are spans of double-stranded genomic DNA -- they don't have an inherent strand like genes etc. However, if the forward strand sequence of the region aligns to the reverse strand of the other region, then the relative orientation is '-'. And that's a reciprocal relationship. So say region A has other-region B, + and - are the stranded sequences, and ~ means "aligns to": +A ~ +B <==> -A ~ -B <==> relative orientation = + -A ~ +B <==> +A ~ -B <==> relative orientation = - 3) We suggest checking the references listed in the description page for more details (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=genomicSuperDups) or contacting the authors (the email is on the description page also), but on of our engineers thinks that based on this statement in the description page's Methods section (emphasis added): The repeats were then reinserted into the pairwise alignments, the ends of alignments trimmed, and global alignments were generated. that the trimming of alignment ends might explain the shorter length of the "optimal global alignment." I hope this information is helpful! Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/10/11 9:38 AM, Sampath, Srirangan wrote: > Below are some questions regarding hg18 Seg-dup tracks. > > 1) I am using Table browser to download the 'genomicSuperDups' and using 'all > fields from selected table' to extract all the fields in the schema. There is > 1bp shift in the 'chromStart' and 'otherStart' columns between the data > downloaded from Table Browser and the corresponding information from the > Genome Browser. The start positions of the intervals in Genome Browser is > shifted one base ahead of the Table Browser. The End positions do match. Why > is that and which one is correct? > > Below I have pasted the both the Table Browser rows and the corresponding > link to the Genome Browser > > Table Browser: > bin chrom chromStart chromEnd name score strand otherChrom otherStart > otherEnd otherSize uid posBasesHit testResult verdict chits ccov alignfile > alignL indelN indelS alignB matchB mismatchB transitionsB transversionsB > fracMatch fracMatchIndel jcK k2K > 118 chr10 47833296 47862414 chr10:45491750 419130 + chr10 45491750 45520834 > 135374737 0 1000 N/A N/A N/A N/A align_both//0004/both020825 28953 63 298 > 15276 28292 661 457 204 0.97717 0.975048 0.0231848 0.0232378 > > Genome Browser: > http://www.genome.ucsc.edu/cgi-bin/hgc?hgsid=206552079&o=47833296&t=47862414&g=genomicSuperDups&i=chr10%3A45491750 > > > 2) There is a column with 'strand' information on the 'genomicSuperDups' > schema (Table Browser). But there is no 'Other Position Relative Orientation' > data. Is the 'strand' column from Table Browser the actual strand information > of the sequence, or relative orientation of the 'other position'? From the > Table Browser output when I manually checked a few, all '+' seem to have '+' > relative orientation of the other position , and all '-' seem to have '-' > relative orientation of the other position. > > > 3) Sometimes the link to the 'Optimal Global Alignment' does not provide the > Alignment for the entire interval. For example, the track for > Item: chr10:48284311 > is 428kb long. But the 'Optimal Global Alignment' provides alignment for only > 103 kb. Below are the links > > http://www.genome.ucsc.edu/cgi-bin/hgc?hgsid=206563651&o=45896971&t=46325469&g=genomicSuperDups&i=chr10%3A48284311 > http://humanparalogy.gs.washington.edu/build36/align_both//0004/both020916 > > > > Thank you, > Sri. > > > > Dr. Srirangan Sampath Ph.D., > ABMG Clinical Cytogenetics Fellow > Medical Genetics Laboratories > Department of Molecular& Human Genetics > John P. McGovern Campus NABS-O250 > Baylor College of Medicine, > Houston, TX-77021 > Cell: 504-390-5512 > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
