Genomic Intervals Masked by WindowMasker + SDust
 
Position: CM023913.1:51504838-51504858
Genomic Size: 21
View DNA for this feature (GCA_013407035.1/ASM1340703v1 Jul. 2020)
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Description

This track depicts masked sequence as determined by WindowMasker on the the 13 Jul 2020 Coloeus monedula/GCA_013407035.1_ASM1340703v1/GCA_013407035.1 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_013407035.1_ASM1340703v1.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCA_013407035.1_ASM1340703v1.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 199,426,567 bases in the assembly size 1,035,863,955 for a percent coverage of % 19.25.

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