Originally posted by sunhh
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Thank you very much!
lyn
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cat /group/aquaculture/mussels/sequencing/MUSSEL1/repeatscout/contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout | ./filter-stage-1.prl > contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout.filter1
filter-stage-1.prl
cat /group/aquaculture/mussels/sequencing/MUSSEL1/repeatscout/contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout | ./filter-stage-1.prl > contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout.filter1
./build_lmer_table -l 14 -sequence yourgenome.fasta -freq ~/Desktop/Vi_14.freq
./RepeatScout -sequence yourgenome.fasta -output your_repeats.fasta -freq your_freq_table -l 14
cat your_repeats.fasta| ./filter-stage-1.prl >your_repeats_filtered1.fasta
./RepeatMasker -s -lib your_repeats_filtered1.fasta yourgenome.fasta
cat your_repeats_filtered1.fasta | ./filter-stage-2.prl --cat yourgenome.fasta.out --thresh 10 your_repeats_filtered2.fasta
./RepeatMasker -pa 4 -s -lib your_repeats_filtered2.fasta -nolow -norna -no_is -gff yourgenome.fasta
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