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OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
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polyA trimming #179

Open nservant opened 5 years ago

nservant commented 5 years ago

Hi there, Thank you for developing fastp. I try to run it on a 3'seq experiment (without any option for polyA trimming), and fastp i) does not detect any adapters, ii) does not trim any reads. And in practice, I know that I do have many reads spanning the polyA tail and then the adapter sequence, as this one CCCAACGAAACTAGACGAGCTAACTAAGAATAGCTAAAAGAGCACACCCGTCTATGTAGCAAAAAAAAAAAAAAAAAAGATCGGAAGAGCAACCGTCTGAA So, is there any parameter to add, so that it can detect such case ? Thanks Here is the command line I used : fastp --qualified_quality_phred 0 --disable_trim_poly_g --length_required 10 -i input.fastq.gz -o input_trimmed.fastq.gz -j input.fastp.json -h input.fastp.html --thread 2 Nicolas

sfchen commented 5 years ago

Em, polyA may affect adapter detection, I will check that.

If you know the adapter, you can specify it by --adapter_sequence option directly