Hello Tapas, These methods are extracting data from two sources. One is the backend data table, the other the browser display. Coordinates in the data table use a "0-based" start position - add +1 to get the "1-based" start position, as described in this FAQ:
Database/browser start coordinates differ by 1 base http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 When examining data aligned to the reverse strand, the coordinates in the data table are still organized smallest->largest genome coordinate. Meaning, the stop (smallest coordinate) will have the +1 added. This can be a bit confusing, but if you are interested in the details, this additional FAQ can be helpful to review: Coordinate Transforms http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Please feel free to contact the mailing list support team again if you would like more assistance. Warm regards, Jen UCSC Genome Browser Support On 8/3/10 11:36 PM, [email protected] wrote: > Respected Sir, > I am a research fellow at Indian Statistical Institute, Kolkata, > India. I am currently involved in Bio-informatics research. > Currently I am searching for chromosomal location of microRNAs. > > I have found that there is two ways that gives the desired > information. First way to find required information is -> (i) > goto http://genome.ucsc.edu/cgi-bin/hgTables , (ii) put clade : > Mammal, genome : Human, assembly : Mar. 2006 (NCBI36/hg18), > group: Genes and Gene Prediction Tracks, track : sno/miRNA , > table: wgRna . > Second one is -> i) goto > http://genome.ucsc.edu/cgi-bin/hgGateway, (ii) put clade: > Mammal, genome: Human, assembly: Mar. 2006 (NCBI36/hg18), > position: genename (user input), gene: blank, image width: > 800(default). > > For example : miRNA - hsa-mir-216a > 1st one gives : chr = 2 , chromStart = 56069588 chromEnd = 56069698 > 2nd one gives: chr2:56,069,589-56,069,698. > > But the 2 ways gives everything right except chromStart. If > first one gives its value equal to x then second one gives its > value equal to x+1. Please give me the information regarding > which one is correct > > Thanking you, > Yours faithfully, > Tapas Bhadra > Senior Research Fellow, > ISI Kolkata > > This mail is scanned by Ironport > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
