Porechop(2)

We need to run the following command:

porechop

with the following parameters

Go to your data_artic directory first:

cd ~/workdir/data_artic/

Then run porechop:

porechop -i ~/workdir/data_artic/basecall_tiny.fastq.gz -t 14 -v 2 -o ~/workdir/data_artic/basecall_tiny_porechopped.fastq.gz |tee ~/workdir/data_artic/porechop.log

Task: Inspect the log file -have adapters been removed?

And finally, run FastQC again, to compare with the untrimmed data:

mkdir ~/workdir/fastqc/basecall_tiny_trimmed/
fastqc -t 14 -o  ~/workdir/fastqc/basecall_tiny_trimmed ~/workdir/data_artic/basecall_tiny_porechopped.fastq.gz