Which repeats are present in soft-masked sequence?

Question

[Leszek]

I'm using soft-masked version of the zebra fish genome from Ensembl v80.

I would like to know which repeats are in softmasked regions. Is there some easy way of getting this information? Or I should run repeat-masker myself?

Answer 1

[Pierre Lindenbaum]

Under http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/, you can find simpleRepeat.txt.gz (and the schema in simpleRepeat.sql)

585    chr1    6480    6509    trf    3    9.7    3    100    0    58    68    31    0    0    0.89    AAC
585    chr1    6811    6856    trf    2    22.5    2    100    0    90    51    0    48    0    1    AG
585    chr1    7006    7048    trf    2    21    2    100    0    84    50    50    0    0    1    CA
585    chr1    7590    7709    trf    14    8.8    14    81    7    102    33    48    16    0    1.52    GCACACACACGCAC
585    chr1    7591    7670    trf    4    19.8    4    92    0    68    36    50    12    0    1.41    CACA
585    chr1    7591    7719    trf    10    12.8    10    79    6    98    34    48    15    1    1.55    CACACACGCA
585    chr1    7593    7682    trf    18    5.1    18    87    4    101    33    50    15    0    1.45    CACACACACGCACGCACG

[Leszek]

Thanks Pierre! Actually, I'm more interested in http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/nestedRepeats.txt.gz!