WM + SDust Track Settings
 
Genomic Intervals Masked by WindowMasker + SDust   (All Variation and Repeats tracks)

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Description

This track depicts masked sequence as determined by WindowMasker on the the 21 Feb 2020 Amblyraja radiata/GCF_010909765.2_sAmbRad1.1.pri/GCF_010909765.2 genome assembly. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site.

Methods

To create this track, WindowMasker was run with the following parameters:

windowmasker -mk_counts true -input GCF_010909765.2_sAmbRad1.1.pri.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCF_010909765.2_sAmbRad1.1.pri.unmasked.fa -output windowmasker.intervals
perl -wpe 'if (s/^>lcl\|(.*)\n$//) { $chr = $1; } \
   if (/^(\d+) - (\d+)/) { \
   $s=$1; $e=$2+1; s/(\d+) - (\d+)/$chr\t$s\t$e/; 
   }' windowmasker.intervals > windowmasker.sdust.bed
The windowmasker.sdust.bed included masking for areas of the assembly that are gap. The file was 'cleaned' to remove those areas of masking in gaps, leaving only the sequence masking. The final result covers 1,336,970,073 bases in the assembly size 2,558,784,953 for a percent coverage of % 52.25.

References

Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941