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Update fastqc_per_base_sequence_quality_dropoff.py #135

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ksilnoaa opened this issue Jul 8, 2024 · 2 comments
Open

Update fastqc_per_base_sequence_quality_dropoff.py #135

ksilnoaa opened this issue Jul 8, 2024 · 2 comments

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@ksilnoaa
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ksilnoaa commented Jul 8, 2024

Update fastqc_per_base_sequence_quality_dropoff.py to work with fastq_summary.qzv output

@ksilnoaa ksilnoaa changed the title Update script Update fastqc_per_base_sequence_quality_dropoff.py Jul 8, 2024
@lukenoaa
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lukenoaa commented Jul 9, 2024

I agree it would be great if this script can work directly from QIIME output without running FastQC/MultiQC. The zip archive of fastq_summary.qzv does contain forward-seven-number-summaries.tsv and reverse-seven-number-summaries.tsv that contain the distribution of quality scores at each position. For example, we could have the script report at which position the 9th percentile drops below a quality score of 20.

@ksilnoaa
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@lukenoaa yes that's what I was thinking! Would you be able to adapt that script for that functionality? Then I can include it in the V2 workflow.

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