Per Steven’s GitHub Issues request, I ran FastQC on the Eastern oyster MBD bisulfite sequencing data we recently got back from ZymoResearch.

Ran FastQC locally with the following script: 20180409_fastqc_Cvirginica_MBD.sh

#!/bin/bash
/home/sam/software/FastQC/fastqc \
--threads 18 \
--outdir /home/sam/20180409_fastqc_Cvirginica_MBD \
/mnt/owl/nightingales/C_virginica/zr2096_10_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_10_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_1_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_1_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_2_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_2_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_3_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_3_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_4_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_4_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_5_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_5_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_6_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_6_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_7_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_7_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_8_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_8_s1_R2.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_9_s1_R1.fastq.gz \
/mnt/owl/nightingales/C_virginica/zr2096_9_s1_R2.fastq.gz

MultiQC was then run on the FastQC output files.

All files were moved to Owl after the jobs completed.

Results:

FastQC Output folder: 20180409_fastqc_Cvirginica_MBD/

MultiQC Output folder: 20180409_fastqc_Cvirginica_MBD/multiqc_data/

MultiQC report (HTML): 20180409_fastqc_Cvirginica_MBD/multiqc_data/multiqc_report.html

Everything looks good to me.

Steven’s interested in seeing what the trimmed output would look like (and, how it would impact mapping efficiencies). Will initiate trimming.

See the GitHub issue linked above for the full discussion.