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