eed5b92e1fea673976546c6cdfe47a9414a9c33a lrnassar Thu Mar 31 15:49:42 2022 -0700 Updating assembly to correct hg38, refs #29189 diff --git src/hg/makeDb/trackDb/humanChainNet.html src/hg/makeDb/trackDb/humanChainNet.html index 28c5691..e06f705 100644 --- src/hg/makeDb/trackDb/humanChainNet.html +++ src/hg/makeDb/trackDb/humanChainNet.html @@ -1,48 +1,48 @@ <H2>Description</H2> <H3>Chain Track</H3> <P> -The chain track shows alignments of human (Feb. 2009/hg19) to the +The chain track shows alignments of human (GRCh38/hg38) to the $organism genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and $organism simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. <P> The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the $organism assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the $organism genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.</P> <P> In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.</P> <H3>Net Track</H3> <P> The net track shows the best human/$organism chain for every part of the $organism genome. It is useful for finding orthologous regions and for studying genome rearrangement. The human sequence used in this annotation is from -the Feb. 2009 (hg19) assembly.</P> +the GRCh38/hg38 assembly.</P> <H2>Display Conventions and Configuration</H2> <H3>Chain Track</H3> <P>By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.</P> <P> To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.</P> <H3>Net Track</H3> <P> In full display mode, the top-level (level 1)