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
