DNA sequencing QC
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Filter Options

Output filtered data

So far, we focused on using fastp to evaluate data quality. But if we want to use the filtered data in downstream analyses, we need to save the filtered FASTQ files for later processing. To do so, we can use the --out parameters:

fastp --in1 HG004_R1.fastq.gz --in2 HG004_R2.fastq.gz --out1 HG004_R1_filtered.fastq.gz --out2 HG004_R2_filtered.fastq.gz

This creates the original HTML/JSON reports, along with a filtered FASTQ file for each input: . Notice that FASTQ files with filtered in their filenames are smaller, as expected.

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