Hello Peng, You will want your data in SAM/BAM format for best display results. Many tools that align paired end read sequences can produce SAM/BAM as output but you can also find a number of converters here:
http://samtools.sourceforge.net/swlist.shtml Once you have things in SAM/BAM format you can find instructions for making a BAM custom track here: http://hgwdev.cse.ucsc.edu/goldenPath/help/bam.html Note that Bed12 format can show the paired ends (same as in #3959) but if the alignment tool can directly produce SAM/BAM, that's best since you'll be able to see mismatches, and clicking into details will show additional info if the aligner has added, if any (tags, quality etc). Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/7/11 11:30 AM, Peng Yu wrote: > Hi, > > I don't see how to display paired end reads, except converting them > into bed format. But as far as I know bed format is not designed for > paired end reads. Does anybody know a better way to display paired end > reads in the genome browser? Thanks! > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
