Hi there, I was trying to analyse few data sets of A. thaliana through the UCSC Genome Browser and found that the help menu did not answer many of my questions. Firstly, the documentation is incomplete on how to add custom annotation tracks into the browser (only for the A. thaliana (Arabidopsis thaliana) Genome Browser Gateway). Secondly, I was wondering on to what specific formats the Genome Browser would accept A. thaliana data because the Human Genome Browser suggests bedGraph<http://genome.ucsc.edu/goldenPath/help/bedgraph.html>, GTF<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GTF>, PSL<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#PSL>, BED<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED>, bigBed<http://genome.ucsc.edu/goldenPath/help/bigBed.html>, WIG<http://genome.ucsc.edu/goldenPath/help/wiggle.html>, bigWig<http://genome.ucsc.edu/goldenPath/help/bigWig.html>, BAM<http://genome.ucsc.edu/goldenPath/help/bam.html>, VCF<http://genome.ucsc.e! du/goldenPath/help/vcf.html>, MAF<http://genome.ucsc.edu/goldenPath/help/maf.html>,BED detail<http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7>, Personal Genome SNP<http://genome.ucsc.edu/FAQ/FAQformat.html#format10>, and microarray<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#microarray> (BED15). Would it be possible to use these formats for the A. thaliana Genome Browser.
Kindly could you clear my questions. I appreciate the concern. Best Regards Akshay _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
