Hello again, Jeremy, I'm glad you got your files converted to MAF.
I'm not sure what you mean by "shade the background". If you mean the background of the entire track, the answer is no. If you mean, you would like to change the yellow highlighting to a different color, then the answer is also no. If you mean, you would like to change the alternating colors of the checkerboard pattern when coding frames are turned on, then the answer is also no. However, you could probably hack "background shading" for all three cases if you built your own mirror and edited the C code. So, yes, you would have a lot more control if you had your own mirror site. As for the question about the quality score, note this line in the description page for any Conservation track: "Pairwise alignments of each species to the human genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons." So, the quality score does affect the display of the resulting track, but in the case of the UCSC Conservation tracks, it does not come from the "q" line in the MAF file. Instead, the pairwise scores are calculated on the fly for the density plots (except if you're zoomed out over 1mb when the mafSummary table is used which has pairwise scores in it). I hope this information is helpful to you. Please don't hesitate to contact the mail list again if you require further assistance. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Jeremy Davis-Turak wrote: > Hi Ann, > > Thanks for your response. I am using the website, not a mirror. I > converted my files to MAF and it worked well. > > The only thing left is cosmetic - I was wondering if it were possible > to shade the background a different color. Also, I noticed the MAF > file can include a quality score, but I can't figure out how the > quality score affects the output (like changing the color or > something). > > If I were to use a mirror, would I have more control in manipulating > such things? > > Thanks, > > Jeremy > > > > On Tue, Jan 6, 2009 at 11:50 AM, Ann Zweig <[email protected]> wrote: >> Hi Jeremy, >> >> If you are running a mirror of our genome browser, then you should be able >> to create such a track. If that's the case, let us know and we can give you >> more detailed instruction. Here's the information about creating a mirror: >> http://genome.ucsc.edu/admin/mirror.html >> >> The Genome Browser and Blat software are free for academic, nonprofit, and >> personal use. A license is required for commercial use. >> >> If you are, instead, trying to do this using our website and source code >> tools, I cam give you some pointers to get that done. You will use two kent >> source tools: pslPretty and axtToMaf. In general (for PSL -> MAF >> translation): >> >> pslPretty -axt | axtToMaf >> >> See this previously-answered mail list question for more details: >> http://www.soe.ucsc.edu/pipermail/genome/2008-November/017574.html >> >> You may have to make a few edits to the resulting MAF file in order to >> display it as a Custom Track. Read more about creating a MAF Custom Track >> here: http://genome.ucsc.edu/FAQ/FAQformat.html#format5 >> >> >> I hope this information is helpful to you. Please don't hesitate to contact >> the mail list again if you require further assistance. >> >> >> Regards, >> >> ---------- >> Ann Zweig >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> >> >> >> >> Jeremy Davis-Turak wrote: >>> Hi, >>> >>> I'm trying to create a track of aligned Illumina sequencing reads. >>> Currently I am using a .BED file, but I am having trouble with >>> displaying the mismatches in those alignments. I would like to have >>> them look just like the BLAT alignment results, where mismatches have >>> a changed base, and indels are shown. However, the PSLX format does >>> not seem to be supported. I noticed that the BLAT results are a >>> combination of a .FA file and and a .PSL file. Is there any support >>> for creating combining these files, outside of using BLAT? >>> >>> Thanks, >>> >>> Jeremy >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
