On Fri, Jun 18, 2010 at 11:36 AM, Hiram Clawson <[email protected]> wrote: > Please note what the -mask argument says in the help message: > > -mask=type Mask out repeats. Alignments won't be started in masked region > but may extend through it in nucleotide searches. Masked areas > are ignored entirely in protein or translated searches. Types are > lower - mask out lower cased sequence > upper - mask out upper cased sequence > out - mask according to database.out RepeatMasker .out > file > file.out - mask database according to RepeatMasker file.out > > Therefore, if you do not want alignments to start in masked areas of the > genome, > then use -mask=lower with the mm9.2bit file. The mm9.2bit file indicates > masked regions with lower case letters. I guess the question would be, why > do you specifically want to exclude starting alignments in masked areas of > the genome ? Are your query sequences designed to never be in repeats and > therefore should not be in repeats ? Have you tried running the blat > command > with mm9.2bit as the 'database', your sequences as the 'query' and viewing > the resulting output.psl file in a custom track ? Try it without arguments > to see what you obtain. Use pslFilter on your output.psl file to limit your > results to desired criteria. There are over 30 other psl manipulation > programs > available to work with your raw output. > > To visualize your results, take your psl output from your blat result and > submit that as custom track input. Then you can see all of your alignments > and you are in complete control of how you use blat.
I think that you misunderstand what I mean by "visualization". I knew that I can convert the psl to bw or bb format. But this is not what I am looking for. I want to visualize the raw mapped sequences, just as if I paste the sequence on the following page and get the a page with links to the sequences showing in the genome browser. http://genome.ucsc.edu/cgi-bin/hgBlat?command=start I had uploaded the sequences manually to the above address. But I just get bored of doing so. I'd like there is an better way to look at the sequences in the browser without having to upload the sequences each time. Since I can use custom track by clicking a url, I think that there might be a way to do the similar thing for visualizting blat result. You have mentioned gfClient and gfServer in the other thread. But I can not really look at too many blat results in the browser by my naked eye. Therefore, this is not going to be a load problem to the server. > On another note, if you would like to study how we operate blat here, you > can > see over 500 examples of blat commands in our 'make doc' which is a record > of every procedure we perform here to produce the genome browsers. Studying > these examples will give you a good idea of how blat is used and different > ways of using the arguments to achieve desired results. In your copy of the > kent > source tree, go to: src/hg/makeDb/doc/ and run a grep for "blat " on *.txt > in that directory. Look at the lines from that result to see typical blat > operations. I checked it. There are too many irrelevant stuffs there, which is hard for me to completely understand at this time. May I suggest to get the most important examples documented on the genome browser website for the purpose of explanation of the command option syntax. As of now the help page printed by blat without arguments seems a little bit sparse, some of explanations of the options could be explained in more details to avoid any unnecessary confusions. -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
