This is a test version of Biostars. For the public version, visit https://www.biostars.org.
repeatMasker parameter for primer design

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 ?

repeatmasker primer design
• 1,667 views • link
written by Nicolas Beaume • Nicolas Beaume

1 answer

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)

• 0 views • link
written by Nicolas Beaume • Nicolas Beaume

Log in to answer this question.

More posts like this