From 7e144ec1d8817a6363beaed77e5c03ddbcc0c43c Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Mon, 13 Feb 2023 05:26:02 +0100 Subject: [PATCH] Update Wolf tutorial with the OBITools3 --- Wolf-tutorial-with-the-OBITools3.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Wolf-tutorial-with-the-OBITools3.md b/Wolf-tutorial-with-the-OBITools3.md index edd3840..d33107f 100644 --- a/Wolf-tutorial-with-the-OBITools3.md +++ b/Wolf-tutorial-with-the-OBITools3.md @@ -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