Description
This track depicts masked sequence as determined by WindowMasker on the
the 14 May 2019 Setaria viridis/GCF_005286985.1_Setaria_viridis_v2.0/GCF_005286985.1 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 GCF_005286985.1_Setaria_viridis_v2.0.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCF_005286985.1_Setaria_viridis_v2.0.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 115,231,343 bases in the assembly size 395,869,604 for
a percent coverage of % 29.11.
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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