Joshi, Yes, you do need to use an appropriate assembly for your custom track. You can toggle which assembly at the top of the page where you enter your custom track. Also, it is not sufficient to give the url of this maf, because a header line is required. Please see these instructions on making a custom maf track:
http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Note this line, in the instructions: "The first track line is necessary for custom tracks, but should be removed otherwise." I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group T Joshi wrote: > Hi, > I have a MAF alignments of 5 vertebrates downloaded from UCSC ( > http://hgdownload.cse.ucsc.edu/goldenPath/phastConsPaper/vertebrate-mafs.tgz). > I tried extracting regions through custom track. Upon submitting the file or > even the URL to "add custom track" , I got error similar to this : > > Unrecognized format line 2 of custom track: a score=259.0 (note: chrom names > are case sensitive) * > > *Is this problem due to different assembly versions? > > My second question might not be relevant for UCSC but at least for the users > of MAF. I have a set of subsequences from Human genome, for which I want to > check conservation using the above MAF alignments. Which tools are suitable > for this task ? Is there any local alignment program in your knowledge ? > > Thanking you in anticipation... > Joshi > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
