Extract sequences from fasta EXCEPT regions given in the bed file
I want to extract sequences from a genome.fasta, EXCLUDING the regions listed in the Bed file. So I need an output fasta file that does not contain the regions present in the Bed file. See For example:
cat genome.fasta
chr1
ATCGGAGTCGAATTCAATCTT
cat bed.txt
chr1 6 17
cat my_ouput.fasta
chr1
ATCGGA
chr1
TCTT
I tried Bedtools getfasta and intersect commands, but it seems they do not have any option to fulfill my need. I would appreciate any suggestion or a script. Thank you.
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farhan.phd.unesp •
2 answers
perhaps combine bedtools complement with bedtools getfasta?
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Friederike
Thanks so much ! The bedtools complement worked. Amazing..
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farhan.phd.unesp •
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