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You can use TRF2GFF to convert the trf dat file to gff3 and then use bedtools getfasta to extract the gff intervals from your genome fasta.
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TFR output alignment into fasta?
Hi There,
Does anyone know how to convert the output alignment results from Tandem repeat finder (https://tandem.bu.edu/trf/trf.html) into a fasta representation (fasta, clustal, etc...).
I have check some parsers, like convert the .dat file into gff, though nothing about turning the alignment (http://tandem.bu.edu/trf/trf.definitions.html#alignment) into some fasta file; which from my perspective would be a better ideal representation. ThanksTags: None
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