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czbiohub-sf / sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
GNU Affero General Public License v3.0
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skip trimming primers #67

Open nhatas opened 4 years ago

nhatas commented 4 years ago

I have sequencing data generated with TruSeq primers. Is there a way to skip the primer trimming step? Can I feed in an empty bed file? I tried feeding in a FASTA file of TruSeq primers but that resulted in an error.

jackkamm commented 4 years ago

Hi,

Currently there's no way to skip the primer trimming step. However, it will only trim ARTIC/MSSPE primers at the ends of reads, so it should only have a minimal impact -- reads that happen to start/end right at those locations will lose 10-15 bases, but most reads will be unaffected.

Still, I will leave this issue open as a feature request to skip the primer trimming skip.

TruSeq adapters are automatically trimmed by the pipeline so you don't need to worry about providing those.