... | @@ -131,11 +131,11 @@ For EMBL files, you can give the path to a directory with several EMBL files. |
... | @@ -131,11 +131,11 @@ For EMBL files, you can give the path to a directory with several EMBL files. |
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obi grep --require-rank=species --require-rank=genus --require-rank=family --taxonomy wolf/taxonomy/my_tax wolf/v05_refs wolf/v05_refs_clean
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obi grep --require-rank=species --require-rank=genus --require-rank=family --taxonomy wolf/taxonomy/my_tax wolf/v05_refs wolf/v05_refs_clean
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2. Dereplicate identical sequences:
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2. Dereplicate identical sequences (note: not a necessary step, avoid for big databases as long as #79 is not fixed):
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obi uniq --taxonomy wolf/taxonomy/my_tax wolf/v05_refs_clean wolf/v05_refs_uniq
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obi uniq --taxonomy wolf/taxonomy/my_tax wolf/v05_refs_clean wolf/v05_refs_uniq
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3. Ensure that the dereplicated sequences have a taxid at the family level:
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3. Ensure that the dereplicated sequences have a taxid at the family level (if you ran the previous step):
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obi grep --require-rank=family --taxonomy wolf/taxonomy/my_tax wolf/v05_refs_uniq wolf/v05_refs_uniq_clean
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obi grep --require-rank=family --taxonomy wolf/taxonomy/my_tax wolf/v05_refs_uniq wolf/v05_refs_uniq_clean
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