How Can I Get The Location Of Assembly Gaps And Centromere In Hg19 ?

Question

[siyu]

when I use ucsc , I feel that the centromere I find is a part of gaps?? is it true?

I use FILTER "centromere" in gap.

Answer 1

[Pierre Lindenbaum]

for the centromers, see this previous question:

How can I get the human chromosome centromere position and chromosome length in GRCh37/hg19

for the gaps, see the tables gap in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz

SQL type     info     description
bin     585    smallint(6)     range     Indexing field to speed chromosome range queries.
chrom     chr1    varchar(255)     values     Reference sequence chromosome or scaffold
chromStart     0    int(10) unsigned     range     start position in chromosome
chromEnd     10000    int(10) unsigned     range     end position in chromosome
ix     1    int(11)     range     ix of this fragment (useless)
n     N    char(1)     values     always 'N'
size     10000    int(10) unsigned     range     size of gap
type     telomere    varchar(255)     values     contig, clone, fragment, etc.
bridge     no    varchar(255)     values     yes, no, mrna, bacEndPair, etc.

[PoGibas]

Pierre, I just noticed, isn't your link for "gad", but not "gap"? :-)

Shouldn't it be http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz

[Pierre Lindenbaum]

fixed: thanks