Hello, When I originally answered your question, I was misleading when I stated that there were no alignment data in the database, because there are a few tables in MAF format. However, none are linked to SNP data directly and I thought that SNP was your data of interest. The file I referred you to has two sequence strings in it per row - one for the baseline genome and one for the rs SNP variation sequence. I thought that this would be useful because the two sequences could be stacked into an alignment (using your own tools) to view the variation.
But you are correct, for certain MAF-containing data tracks, alignment data in the Table browser can be preserved when performing an intersection against another track (such as SNPs). For others, only positional information is possible. And with either, the name of the data point used as a position for an intersection is not in the output, only rows from the original table are in the output. Here is a link to our help section for these types of alignments: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA Example where alignment data is preserved using TB: Initial track: Conservation, table: multiz44way (any other table from this track will not produce alignment output using the intersection function) Intersection track: SNPs (129) Must choose an intersection from the section: Intersect multiz44way items with bases covered by SNPs (129) Any other intersection will return positional data only But, the problem with output is that you do not know which SNPs were overlapped or where they are located in the output. One solution is to do one SNP at a time and name the output with snp name & position. Another option is to use Galaxy. Under "fetch alignments" are several MAF tools. Another popular tool is "Join the intervals of two queries side-by-side" under "Operate on Genomic Intervals". You may find a way to merge the data and fetch alignments while preserving track annotation from both the query and the target track. We hope this helps, Jennifer Jackson UCSC Genome Bioinformatics Group Revak Raj Tyagi wrote: > Hi Jennifer, > > Thank you for the clarification. I have another question. Table Browser > allows downloading of CDS FASTA alignments for tracks like UCSC genes > and refSeq genes. How does this part interacts with the database? Can > this be linked with positions obtained from SNPs table? > > Thank you, > With regards, > > > Revak Raj Tyagi > > The Biodesign Institute > Arizona State University > > On Mon, 2009-02-16 at 14:07 -0800, Jennifer Jackson wrote: > >> Hello, >> We do not store alignments in the database. However, there is a file >> that includes some surrounding genomic for data in the dbSNP dataset >> (labeled by the snp identifier) that can be downloaded via ftp. >> >> goldenPath/hgFixed/database/dbSnpRsHg.txt.gz >> >> Instruction for using ftp: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 >> >> Thank you, >> Jennifer Jackson >> UCSC Genome Bioinformatics Group >> >> Revak Raj Tyagi wrote: >> >>> Hi, >>> >>> I want to download alignments of regions around some SNP sites (~2000). >>> Can someone please guide how this can be done? I already have the >>> positions using SNPs table in Table Browser, but it doesn't give option >>> for downloading alignments. >>> >>> Thank you, >>> With regards, >>> >>> >>> Revak Raj Tyagi >>> >>> The Biodesign Institute >>> Arizona State University >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome >>> >>> > > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
