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  • Wolf tutorial with the OBITools3

Wolf tutorial with the OBITools3 · Changes

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Update Wolf tutorial with the OBITools3 authored Feb 13, 2023 by Celine Mercier's avatar Celine Mercier
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Wolf-tutorial-with-the-OBITools3.md
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......@@ -17,7 +17,7 @@ And unzip it:
`--quality-solexa` is the appropriate fastq quality option because it's an old dataset, `wolf_tutorial/wolf_F.fastq` is the path to the file to import, `wolf` is the path to the DMS that will be automatically created, and `reads1` is the name of the view into which the file will be imported.
**Note:** If some sequences fail to import, you might need to use the `--input-na-string` option to define the NA string.
**Note:** If some sequences fail to import, you might need to use the `--input-na-string` option to define the string for NA values.
2. Import the second set of reads:
......@@ -138,6 +138,8 @@ Otherwise, to build the database yourself from the start:
obi import --taxdump taxdump.tar.gz wolf/taxonomy/my_tax
**Note:** You can use `obi addtaxids` to annotate sequences with their NCBI taxids, guessed from the taxon name. You can also use `obi taxonomy` to add your own taxa to a taxonomy.
5. Use ecoPCR to simulate an *in silico* PCR with the V05 primers:
obi ecopcr -e 3 -l 50 -L 150 -F TTAGATACCCCACTATGC -R TAGAACAGGCTCCTCTAG --taxonomy wolf/taxonomy/my_tax wolf/embl_refs wolf/v05_refs
......
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  • Installing the OBITools3
  • The OBITools3 data structure
  • The OBITools3 syntax
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