ReapeatMasker only uses E. coli insertion elements
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5.7 years ago
Ric ▴ 350

Hi, I used RepeatMasker with different species, but it always only compared to E. coli insertion elements:

    # wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chrM.fa.gz
    # gunzip chrM.fa.gz

    # RepeatMasker -species human -s -xsmall chrM.fa
    RepeatMasker version open-4.0.5
    Search Engine: NCBI/RMBLAST [ 2.2.27+ ]
    Master RepeatMasker Database: /usr/local/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: 20150807 )

    analyzing file chrM.fa

    Checking for E. coli insertion elements
    identifying Simple Repeats in batch 1 of 1
    identifying full-length ALUs in batch 1 of 1
    identifying full-length interspersed repeats in batch 1 of 1
    identifying remaining ALUs in batch 1 of 1
    identifying most interspersed repeats in batch 1 of 1
    identifying long interspersed repeats in batch 1 of 1
    identifying ancient repeats in batch 1 of 1
    identifying retrovirus-like sequences in batch 1 of 1
    identifying Simple Repeats in batch 1 of 1
    processing output: 
    cycle 1 
    cycle 2 
    cycle 3 
    cycle 4 
    cycle 5 
    cycle 6 
    cycle 7 
    cycle 8 
    cycle 9 
    cycle 10 
    Generating output... 
    masking
    done

Do I have to use an addition parameter in order to extend the search? 

 

 

 

 

genome repeatmasker • 2.7k views
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add the -lib option to use specific libraries of repeats

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2.9 years ago
bioinfo • 0

Because it checks in default mode for them. When you want to skip the insertion elements check, you have to give the option -no_is in your string.

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