Hi, Jennifer: I am still trying to figure a little bit more out of the customized track features.
From UCSC genome browser, I can add customized track for a certain region like this one http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr12:110368000-110980000&hgt.customText=http://people.bu.edu/jiehuang/SH2B3.txt, where I can display SNP position together with annotation text. Then from Genome Graphs, I can upload genome-wide data and get customized graph like the one attached. However, this makes me have to create two different types of graphs with two different input data format. Can I instead make them into one? That is, I load annotation text into the genome-wide GENOME GRAPHS, then when I zoom into certain region that genome-wide graph, I will see regional graphs with the annotation text like the one I generated above. Also, in the GENOME GRAPHS graph, the height of each dot is from the P-value or any numerical variable. Can I make the SNP in the regional graph to show the same kind of Y-axis? So, in a word, I am trying to figure out if there is a way to build one graph that has features of both... Best regards, Jie -----Original Message----- From: Jennifer Jackson [mailto:[email protected]] Sent: Thursday, November 05, 2009 3:32 AM To: Huang, Jie (NIH/NHLBI) [F] Cc: [email protected] Subject: Re: [Genome] customized display for certain SNPs in Genome Graphs? Hello, These specific features are not a part of the current functionality, but I will pass on your comments to our scientific development team. Thank you for the suggestions, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jie Huang (NIH/NHLBI) [F]" <[email protected]> wrote: > From: "Jie Huang (NIH/NHLBI) [F]" <[email protected]> > To: [email protected] > Sent: Wednesday, November 4, 2009 12:14:46 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] customized display for certain SNPs in Genome Graphs? > > Hi, it seems that right now I can import a text file with SNP id and P > values into Genome Graphs, and I can specify a distance threshold to > draw connecting lines. My question is: > > > 1. Can I specify different color for different markers based on > according definition in the input file? > > 2. Can I specify connecting lines for specific SNP pairs based > on according definition in the input file? > > 3. Can I show text for the markers besides its color and > position, maybe when mouse over a marker? > > Thank you very much! > > Jie > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome
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