Picking parameters for QC of long-read data?
Hello all,
What is a good heuristic to pick good defaults for my initial QC run? My data is a bunch of reads produced by Nanopore sequencing of metagenomic samples.
As I understand it, my first pass QC should include excluding short fragments and low quality reads, I am doing this filtering with samtools, and generating reports with FastQC. However, I have not found good data on how to pick those values? Currently I'm gong with Q10 and min 100 bp.
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Use a program meant for QC of long reads like
PycoQC(LINK). Since nanopore Q scores are not the same as Illumina, any Q score filtering may not too severe. It may depend on what you are finally trying to do with the data.I am using chopper which is meant for long reads. My goal is to assemble MAGs and map reads back onto them for further analysis.