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Update wolf_tutorial

Celine Mercier
2019-12-12 17:25:23 +01:00
parent 4ccc5b9228
commit 5608cbcd13
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wolf_tutorial.md

@ -47,23 +47,23 @@ And unzip it:
obi less wolf/reads1 obi less wolf/reads1
### 2. Assign each sequence record to the corresponding sample/marker combination ### 2. Recover the full sequences from the partial forward and reverse reads
Unlike the OBITools1, the OBITools3 make it possible to run ngsfilter before aligning the paired-end reads: obi alignpairedend -R wolf/reads2 wolf/reads1 wolf/aligned_reads
obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences -R wolf/reads2 wolf/reads1 wolf/identified_sequences ### 3. Remove unaligned sequence records
### 3. Recover the full sequences from the partial forward and reverse reads
obi alignpairedend wolf/identified_sequences wolf/aligned_reads
### 4. Remove unaligned sequence records
obi grep -a mode:alignment wolf/aligned_reads wolf/good_sequences obi grep -a mode:alignment wolf/aligned_reads wolf/good_sequences
### 4. Assign each sequence record to the corresponding sample/marker combination
obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences wolf/good_sequences wolf/identified_sequences
Note: Unlike the OBITools1, the OBITools3 make it possible to run ngsfilter before aligning the paired-end reads, BUT it is not recommended to do so for usual data, as ngsfilter will not be able to detect and cut out partially sequenced primers.
### 5. Dereplicate reads into unique sequences ### 5. Dereplicate reads into unique sequences
obi uniq -m sample wolf/good_sequences wolf/dereplicated_sequences obi uniq -m sample wolf/identified_sequences wolf/dereplicated_sequences
### 6. Denoise the sequence dataset ### 6. Denoise the sequence dataset