Hello, To be specific about the alignment data, all of this still comes from the same four MAF data files, you are only reaching the data by a different path. Substitute UCSC Genes in the query I gave you last time, intersect with SNPs the same way, select alignments, and submit. The tables in the drop down menu (for hg18, there are 4) are the same no matter which data you intersect against, as long as that type of intersection does not cause the "loss" of alignment data. This is the same set of steps/rules for the Conservation track query I provided. Those same MAF files are in the mySQL client, but your output options are not as restrictive, since you can define your own output in the select statement. This includes adding in labels from other tables that are part of the where and join clauses (which is not possible just using the TB).
Using the mySQL client would be a great solution to output data that is limited in the TB. Any data in the Table browser is also in the mySQL database we provide access to. If a table contains alignment data, then you can certainly perform a join to link that data to any other data with coordinate information. In the select statement, 1) include your original data point plus other key information will help you keep track of it and the MAF data output lines In the from clause, 2) include all tables, includes those you may be joining through that are not in the select statement In the where clause, 3) join the data on common keys or by bounding the coordinates, something like: snp_coordinate_a > maf_coordinate_a and snp_coordinate_b < maf_coordinate_b If you really want a certain alignment, and it is not in the database, perhaps BLAT is a tool you would find helpful. The output can be used to create a custom track. Link to the mySQL client help page: http://genome.ucsc.edu/FAQ/FAQdownloads#download29 However, it is still unclear what data you are trying to get exactly. If you have more questions, please be very specific about what data you want to view and why, so that I can be more specific about what the results will represent versus what you are trying to figure out/visualize. Jennifer Jackson UCSC Genome Bioinformatics Group Revak Raj Tyagi wrote: > Hello Jennifer, > > Thank you. It was really helpful. > > I am also looking into using MySQL client to see if there can be a way > to link tables such that positional data in SNPs(129) table can be used > to get alignment data from other tables that have MAF data. Is it > possible to do the multiz44way intersection SNPs(129) query using the > MySQL client interface? Can the sequence/alignment be fetched using it? > > Also, Table Browser gives an option to download protein or nucleotide > alignment (for refSeq/UCSC genes). Is it possible to download protein > alignments for intersections as well or using MySQL client? > > Thank you, > With regards, > > > Revak Raj Tyagi > > On Tue, 2009-02-17 at 18:27 -0800, Jennifer Jackson wrote: > >> 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
