Hi Vishnu, The main difference between display modes "dense" and "full" is that dense displays all features collapsed into a single line, whereas full displays each feature on a separate line. For more information on track display modes, please see: https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK_CONT
The display modes "dense" and "full" are not applicable when using the Get DNA tool (mask repeat). For the hg19 assembly, the human genome sequence is provided by the Genome Reference Consortium; hg19 corresponds to GRCh37.Statistics for the GRCh37 build assembly can be found on the NCBI Build 37.1 Statistics web page: http://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=9606&build=37&ver=1 The hg18 assembly corresponds to NCBI Build 36.1 (NCBI36), please see: http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg18 You can view both the BAC End Pairs track and Fosmid End Pairs track in the genome browser. You can turn on these tracks by scrolling down to "Mapping and Sequencing Tracks" and changing the display for "BAC End Pairs" and "Fosmid End Pairs" from "hide" to "pack" (or whichever display you choose). Click "Refresh" and you will now see the tracks in the graphical display. More information on the BAC End Pairs track can be found here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=bacEndPairs For more information on the Fosmid End Pairs track, please see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=fosEndPairs At this time, we do not offer any other primer design programs. I hope this information helps. Please contact us again at [email protected] if you have any further questions. Regards, Luvina --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Mishra, Vishnu wrote: > Hi, > > Please let me know the following: > > > 1. What is the difference between repeat masker "Full" and "Dense" > options? > > 2. When I use repeat masker in the Get DNA tool, is it set to "Full" or > Dense"? > > 3. Are the sequence coordinates on UCSC hg19 version identical to NCBI > build 37.2 (current)? > > 4. Are the sequence coordinates on UCSC hg18 version identical to NCBI > build 36 (previous build)? > > In other words, are the coordinates interchangeable and identical coordinates > will pull out identical sequence from both? > > 5. Are BAC/PAC and Fosmid clones tracked on the genome sequence and how > do I view it? > > 6. Is there a primer design program available on UCSC not just blast, > or in silico PCR? > > > Thanks > > Vishnu Mishra > Senior Scientist, Diagnostic Assay Development > Illumina, Inc. > 9885 Towne Centre Drive > San Diego, CA 92121 > Tel: 858-246-8813 > E-mail: [email protected]<mailto:[email protected]> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
