repeatMasker parameter for primer design

Question

[Nicolas Beaume]

Hi everyone

We are using repeatMasker online to mak low repeat regions and noticed that there may have differences between UCSC repeatMasked sequence and repeatMasker on line (default parameters).

2 questions : - I have googled for a benchmark between the two and didn't find any clear answer but is there a consensus about which source (UCSC, repeatMasker on lin, other...) for primer design and which parameters to set ? - in case I want to exactly reproduce UCSC results on repeatMasker online, which parameter should I use ?

[ATpoint]

FAQ

Answer 1

[Nicolas Beaume]

I auto-answered one part of my own question.

to reproduce UCSC repeat-masking I... just took UCSC sequence. To do that automatically, I used twoBitToFa on my genome of interest file (e.g. http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit). It can be also used to querry the UCSC web site directly through an URL-querry (see https://genome.ucsc.edu/goldenPath/help/twoBit.html)