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
References¶
FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Porechop https://github.com/rrwick/Porechop