Hi Peng, There is some information on that page, but it refers to the MAF format itself, not the display:
1. what does '=' mean? "I -- there are non-aligning bases in the source species between chained alignment blocks before and after this block. The browser shows a double line or '=' in base mode." 2. What does the number on the "Gaps" line mean? "n -- there are non-aligning bases in the source and the next aligning block starts in a new chromosome or scaffold that is bridged by a chain between still other blocks. The browser shows either a single line or a double line based on how many bases are in the gap between the bridging alignments." To get a more detailed description of the display, try clicking on a MAF track description for a track that is already part of the Genome Browser, such as this one for 44-way conservation track on hg19 (look for "Gap Annotation"): http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr7&g=cons44way -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/21/11 6:32 PM, Peng Yu wrote: > Hi Pauline, > >> You can find help documentation on the MAF format here: >> >> http://genome.ucsc.edu/FAQ/FAQformat.html#format5 >> >> Note that for any of the file formats you can simply click on the format >> name in the main custom track menu here for more information: >> >> http://genome.ucsc.edu/cgi-bin/hgCustom > > None of these answer my questions > > 1. what does '=' mean? > 2. What does the number on the "Gaps" line mean? > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
