Per Steven’s request, I concatenated our Crassostrea virginica LSU oil spill MBDseq sequencing data and ran FastQC on the concatenated files.

Here’s the list of input files:

2112_lane1_ACAGTG_L001_R1_001.fastq.gz 2112_lane1_ACAGTG_L001_R1_002.fastq.gz 2112_lane1_ATCACG_L001_R1_001.fastq.gz 2112_lane1_ATCACG_L001_R1_002.fastq.gz 2112_lane1_ATCACG_L001_R1_003.fastq.gz 2112_lane1_CAGATC_L001_R1_001.fastq.gz 2112_lane1_CAGATC_L001_R1_002.fastq.gz 2112_lane1_CAGATC_L001_R1_003.fastq.gz 2112_lane1_GCCAAT_L001_R1_001.fastq.gz 2112_lane1_GCCAAT_L001_R1_002.fastq.gz 2112_lane1_TGACCA_L001_R1_001.fastq.gz 2112_lane1_TTAGGC_L001_R1_001.fastq.gz 2112_lane1_TTAGGC_L001_R1_002.fastq.gz

All commands were run on roadrunner (Apple Xserve; Ubuntu 16.04). See Jupyter notebook below for details.

Jupyter notebook (GitHub):

20180910_roadrunner_virginica_fastqc.ipynb

RESULTS:

The concatenated gzip files and FastQC/MultiQC files are in the output folder linked below.

Output folder:

20180910_Cvirginica_oil_fastqc/

MultiQC report (HTML):

20180910_Cvirginica_oil_fastqc/multiqc_report.html