query - self chain track

[Jon Lerga Jaso]

Hello,

I have two quick questions. I am talking about the human genome, assembly hg19.

* Does the self chain track include the segmental dups track information? That is, are the genomic duplications included within the human chained self alignments?

* Are all kind of pairs of inverted repeats included in the self chain track?

Many thanks,

Jon

[Jonathan Casper]

Hello Jon,

Thank you for your questions about the self chain track on the hg19 human genome assembly. In answer to your first question, most but not all of the regions that appear in the segmental duplications track are also marked by the self chain track. 128 of the segmental duplication records (out of roughly 50 thousand) have no overlap with self chains, covering about 400 kb of hg19. Approximately another 600 kb are uncovered by the self chain track, but are covered by segmental duplications that have partial overlaps with the self chain track.

Regarding your second question, the self chain track itself simply contains alignments of the genome assembly against itself, and the individual alignments only proceed in a single direction in the query and target. It does not mark any specific region as an inverted repeat. If you are looking for evidence of an inversion, you will need to combine information from multiple chains. For example, if you find a region where the track contains a large chain with a gap, and the gap is matched to a chain going in the reverse direction near the same destination chromosome position, then that may indicate an inversion. Does that help?

If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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