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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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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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