Description

This track shows which segments of the genome were softmasked for repetitive elements by RepeatMaksker.

Methods

A de novo repeat library was constructed using RepeatScout and the genome was subsequently masked as follows:

build_lmer_table -sequence genome.fa -freq output_lmer.frequency
RepeatScout -sequence genome.fa -output output_repeats.fas -freq output_lmer.frequency
filter-stage-1.prl output_repeats.fas > output_repeats.fas.filtered_1 2> step3.log
RepeatMasker -pa 8 genome.fa -lib output_repeats.fas.filtered_1
cat output_repeats.fas.filtered_1 | filter-stage-2.prl --cat=genome.fa.out > output_repeats.fas.filtered_2
RepeatMasker genome.fa -lib output_repeats.fas.filtered_2 -s -xsmall -pa 10

Credits

The consortium for this project consists of:

• Dannise V. Ruiz-Ramos (Department of Life and Environmental Sciences, 5200 North Lake Road, University of California, Merced, CA 95616, USA)
• Lauren M. Schiebelhut (Department of Evolution and Ecology, One Shields Avenue, University of California, Davis, CA 95343, USA)
• Katharina J. Hoff (University of Greifswald, Institute for Computer Science and Mathematics, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany)
• John P. Wares (Department of Genetics and the Odum School of Ecology, University of Georgia, Athens, GA, USA)
• Michael N. Dawson (Department of Life and Environmental Sciences, 5200 North Lake Road, University of California, Merced, CA 95616, USA)

References

• RepeatMasker: A.F.A. Smit, R. Hubley, and P. Green (2015) RepeatMasker Open-4.0. 2013-2015 http://www.repeatmasker.org.
• RepeatScout: A.L. Price, N.C. Jones and P.A. Pevzner (2005) De novo identification of repeat families in large genomes. Bioinformatics 21(suppl_1):i351-i358, doi:10.1093/bioinformatics/bti1018

Contact for this track data hub: katharina.hoff@uni-greifswald.de