M2 Lab1 - areed37/Andrew_Reed_EPP_531 GitHub Wiki

Run long qc

#1
export PATH=$PATH:/pickett_shared/software/apptainer_unprivileged/bin/

#2
source ~/.bashrc

#3
apptainer exec -B $PWD /sphinx_local/images/longqc_latest.sif* longQC.py --version
# LongQC 1.2.1

#4
apptainer exec -B $PWD -B /pickett_sphinx/projects/EPP531_AGA/lyadav_EPPAGA/sassafras/raw_data/PacBioHiFi/ /sphinx_local/images/longqc_latest.sif* longQC.py sampleqc -x pb-hifi -p 4 -o longqc_out/ ../../lyadav_EPPAGA/sassafras/raw_data/PacBioHiFi/m84109_240206_204137_s2.hifi_reads.bc2017.bam

#No Hifi this week (attach report)