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Update Wolf tutorial with the OBITools3

Celine Mercier
2021-04-28 00:54:16 +02:00
parent 77604f635b
commit e52f9afb58
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Wolf-tutorial-with-the-OBITools3.md

@ -53,11 +53,13 @@ And unzip it:
obi alignpairedend -R wolf/reads2 wolf/reads1 - > aligned_reads.fastq obi alignpairedend -R wolf/reads2 wolf/reads1 - > aligned_reads.fastq
### 3. Remove sequence records with a low overlap alignment score:
We can check the average alignment score (corresponding approximately to the similarity between the sequences in the overlap): We can check the average alignment score (corresponding approximately to the similarity between the sequences in the overlap):
obi stats -a score_norm wolf/aligned_reads obi stats -a score_norm wolf/aligned_reads
### 3. Remove sequence records with a low overlap alignment score: And keep only sequences with a high overlap alignment score:
obi grep -p "sequence['score_norm'] > 0.8" wolf/aligned_reads wolf/good_sequences obi grep -p "sequence['score_norm'] > 0.8" wolf/aligned_reads wolf/good_sequences