Description
This track depicts masked sequence as determined by WindowMasker on the
the 28 Jan 2021 Autographa gamma/GCA_905146925.1_ilAutGamm1.1/GCA_905146925.1 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 GCA_905146925.1_ilAutGamm1.1.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCA_905146925.1_ilAutGamm1.1.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 126,436,545 bases in the assembly size 373,067,087 for
a percent coverage of % 33.89.
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
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