Description
This track depicts masked sequence as determined by WindowMasker on the
the 15 Mar 2023 Agelaius phoeniceus/GCF_020745825.1_Agelaius_phoeniceus_1.1/GCF_020745825.1 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_020745825.1_Agelaius_phoeniceus_1.1.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCF_020745825.1_Agelaius_phoeniceus_1.1.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 301,917,670 bases in the assembly size 1,188,547,179 for
a percent coverage of % 25.40.
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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