How to remove nextera with fastp
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Entering edit mode
9 months ago
Matthias ▴ 50

When run Fastp with

fastp -i in.R1.fastq.gz -o out.R1.fastq.gz -I in.R2.fastq.gz -O out.R2.fastq.gz --detect_adapter_for_pe --disable_quality_filtering --length_required 15

Fastq still detects nextera transposase sequences in the output. Is there a way to remove them with Fastp?

rnaseq nextera fastp ngs • 412 views
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Entering edit mode
9 months ago

Explicitly specify your adapters. Create the adapter file

>nextera
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC

now use the file with the -a flag.

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