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 BGI geoduck FASTQ files to our Mox node (/gscratch/scrubbed/samwhite/bgi_geoduck/).
I ran FASTQC on them to actually check them out and see if they needed any trimming, as I don’t believe this has been done!
FASTQC slurm script: 20180327_fastqc_bgi_geoduck_slurm.sh
Side note: Initial FASTQC failed on one file. Turns out, it got corrupted during transfer! Serves as good reminder about the importance of verifying MD5 checksums after file transfer, prior to attempting to work with files!
This was followed up with MultiQC (run locally from my computer on the files hosted on Owl). This was performed the following day (20180328).
FASTQC output: 20180327_bgi_fastqc
MultiQC output: 20180328_bgi_multiqc
MultiQC HTML report: 20180328_bgi_multiqc/multiqc_report.html
Everything looks nice and clean! Waiting on transfer and FASTQC of Illumina NMP data before proceeding to next assembly attempt.