How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?
2 answers
saving in outfmt6, converting to gtf/bed, and getting upstream sequences with bedtools or bedops.
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shenwei356
You can use the blastdbcmd command to extract sequences (or ranges of it) directly from the blastDBs. Using the tabular blast output (as shenwei356 mentioned as well) will make this more easy.
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lieven.sterck
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