Since running SparseAssembler seems to be working 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.
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
This was followed with MultiQC (locally, after copying the the FastQC output to Owl).
FASTQC output: 20180328_illumina_hiseq_geoduck_fastqc
MultiQC output: 20180328_illumina_hiseq_geoduck_fastqc/multiqc_data
MultiQC HTML report: 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! (probably twice), and see how things change.