Hello, You are correct that the compressed (dense view?) data is not directly available from the Genome Browser Assembly display. But using the Table browser, you can perform a function to collapse duplicated coverage. However, this data will only be a set of coordinates, the primary data (names, etc) will be lost in the data compression. The dense view in the browser is also only a set of coordinates (generated by the Browser cgi).
The tracks that display across intron regions do not actually have the intron sequence as part of the associated mRNA/protein, the introns are a set of coordinates only, based on the the exon/sequence alignments, sometimes annotated in the display based on the detection/quality of the splice sites. Since all display is based on the genomic, there is no way to remove these from the view. These are the basic steps for getting data in a track based on genomic position: 1) Note the genomic region coordinates for your gene of interest 2) Go to the Table browser and set variables: clade, genome, assembly, and region (from step 1) 3) Set variables: group, track then leave the default table as-is 4) Name file and download as gzip or save as custom track and get output These are the basic steps for collapsing (intersecting) data. I am using UCSC Genes as an example: 1) Do 1, 2, and for 3 above, set group: Genes and Gene Predictions, track: UCSC Genes, table: knownGene 2) Click on "Intersect:. Set the group, track, table to be the same as in #3. 3) In the section "Intersect bases covered by UCSC Genes and/or UCSC Genes:" pick the "AND" option. 4) Submit. Set output format: custom track. Click "get output" 5) Adjust the custom track form: select "whole gene" and "get custom track in genome browser". 6) For gene/ mRNA/EST type data, there will be a single data row for every unique/merged exon. For other data such as SNPs, a single row of data for each unique feature. 7) Repeat for other tracks. Download as files or save into a Session. Send to Galaxy for more file comparison options. To filter output of other annotation features (such as SNPs), start with the regular SNP track or the collapsed SNP custom track, and intersect the same way against the base gene track or the collapsed gene track. Click on the help links on the Table browser home page for additional function descriptions and sample queries. We hope this offers you a few more data viewing/downloading options, Jennifer Jackson UCSC Genome Bioinformatics group Adnan Derti wrote: > Hi. > > Is it possible to get the data underlying the GIF displayed by the > Genome Browser, rather than the GIF itself, or in addition to the image? > > Let's say I'm looking at a gene with conservation, transcripts, > expression, SNPs, etc. I'd like to be able to remove introns and > duplicate lines (say, multiple mRNAs & ESTs with identical structures). > Editing the image (i.e., stretching the exons) is feasible but would > distort the data. One option is of course a local installation, and > another is a multitude of mySQL queries, but since queries are done > anyway, is the data stored anywhere, perhaps in trash like the GIF? If > not, is it possible to modify hgTracks or another module to return all > the data behind an image, rather than (or in addition to) the image? I'm > guessing that the answer is negative in each case, but thought I'd ask. > > Thanks. > > Adnan Derti > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
