--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left date: 2018-03-28 21:32:44+00:00 layout: post slug: fastqcmultiqc-illumina-hiseq-genome-sequencing-data title: FastQC/MultiQC – Illumina HiSeq Genome Sequencing Data categories: - 2018 - Geoduck Genome Sequencing tags: - FASTQC - geoduck - Illumina - mox - multiqc - Panopea generosa --- Since running [SparseAssembler seems to be working](https://robertslab.github.io/sams-notebook/posts/2018/2018-03-27-assembly-geoduck-novaseq-using-sparseassembler-kmer-101/) and actually able to produce assemblies, I've decided I'll try to beef up the geoduck genome assembly with the rest of our existing genomic sequencing data. [Yesterday, I transferred our BGI geoduck data to our Mox node and ran it through FASTQC](https://robertslab.github.io/sams-notebook/posts/2018/2018-03-27-fastqcmultiqc-bgi-geoduck-genome-sequencing-data/) I transferred our [Illumina HiSeq data sets (*NMP*.fastq.gz)(https://owl.fish.washington.edu/nightingales/P_generosa/) to our Mox node (/gscratch/scrubbed/samwhite/illumina_geoduck_hiseq). These were part of the Illumina-sponsored sequencing project. I verified the MD5 checksums (not documented) and then ran FASTQC, followed by MultiQC. FastQC slurm script: [20180328_fastqc_illumina_geoduck_hiseq_slurm.sh](https://owl.fish.washington.edu/Athaliana/20180328_illumina_hiseq_geoduck_fastqc/20180328_fastqc_illumina_geoduck_hiseq_slurm.sh) This was followed with MultiQC (locally, after copying the the FastQC output to Owl). ##### Results: FASTQC output: [20180328_illumina_hiseq_geoduck_fastqc](https://owl.fish.washington.edu/Athaliana/20180328_illumina_hiseq_geoduck_fastqc/) MultiQC output: [20180328_illumina_hiseq_geoduck_fastqc/multiqc_data](https://owl.fish.washington.edu/Athaliana/20180328_illumina_hiseq_geoduck_fastqc/multiqc_data/) MultiQC HTML report: [20180328_illumina_hiseq_geoduck_fastqc/multiqc_data/multiqc_report.html](https://owl.fish.washington.edu/Athaliana/20180328_illumina_hiseq_geoduck_fastqc/multiqc_data/multiqc_report.html) Well, lots of fails. I high level of "Per Base N Content" (these are only warnings, but we also haven't received data with these warnings before). Also, they all fail in the "Overrepresented sequences" analysis. I'll run these through [TrimGalore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (probably twice), and see how things change.