Difference between revisions of "Genome masking"
From CoGepedia
(Created page with 'CoGe masks genomes by using NCBI's windowmasker: http://www.ncbi.nlm.nih.gov/pubmed/16287941 Currently, our pipeline for masking is: * Generate frequency counts for the masking ...') |
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Revision as of 10:42, 7 October 2013
CoGe masks genomes by using NCBI's windowmasker: http://www.ncbi.nlm.nih.gov/pubmed/16287941
Currently, our pipeline for masking is:
- Generate frequency counts for the masking database for the genome
- windowmasker -in <genome> -mk_counts -out <counts>
- Mask genome
- windowmasker -in <genome> -ustat <counts> -outfmt fasta -dust T -out <masked genome>
- Convert soft masking (lower case sequence data) to "X".
- CoGe's visualizations often use purple to represent genome sequence "X" to make the identification of masked reasons easy
