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ReapeatMasker only uses E. coli insertion elements

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
• 5,099 views • link
updated by Ram Ram • written by Ric Ric

add the -lib option to use specific libraries of repeats

• 1 views • link
written by lieven.sterck lieven.sterck

1 answer

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.

• 1 views • link
written by bioinfo • bioinfo

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