Does anybody have experience with WindowMasker used on 2nd Gen genomes? I started running it according to the manual (http://www.ncbi.nlm.nih.gov/IEB/Tool...app/winmasker/), but it appears to mask like most of my genome sequence.
This is clearly in contrast to what RepeatModeller and subsequent RepeatMasker produce. They mask about 10% of the genome.
Is there a way to fine tune WindowMasker? Maybe a more comprehensive description than in the manual?
If your goal is to characterize the repetitive fraction of the genome, the software RepeatExplorer seems to produce very good results.
It uses a graph-based clustering approach on a sample of the sequencing reads. It is web based and very easy to use. Softwares that work on assembled genomes have much bias because very similar repeats tend to be collapsed in fewer copies during the assemblage. Using the sequencing reads the only bias you'll have is the sequencing bias itself.
I'm adding links to the publication and the web server. Take a look.
http://bioinformatics.oxfordjournals.org/content/29/6/792
http://repeatexplorer.umbr.cas.cz/
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