Question: Which repeats are present in soft-masked sequence?
0
gravatar for Leszek
3.7 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

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? 

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 3.7 years ago by Leszek4.0k
2
gravatar for Pierre Lindenbaum
3.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

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    CACACACACGCACG
CACG

 

ADD COMMENTlink written 3.7 years ago by Pierre Lindenbaum118k

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

ADD REPLYlink written 3.7 years ago by Leszek4.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1057 users visited in the last hour