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Update Wolf tutorial with the OBITools3

Celine Mercier
2020-05-05 11:12:09 +02:00
parent d9200ca2d5
commit 2c5e82263c
1 changed files with 2 additions and 2 deletions
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Wolf-tutorial-with-the-OBITools3.md

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