/gannet/Atumefaciens/20190923_pgen_fastp_EPI_trimming

Ran fastp to trim an additional 20bp from the 5' end of each read of the EPI geoduck FastQ files.

After trimming on Mox, files were assess with FastQC, followed by MultiQC data summarization.

Files were originally quality/adaptor trimmed with TrimGalore! on 20180516.

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FILES

- 20190923_pgen_EPI_rsync.sh: Bash script used to copy files to Mox and then execute the SBATCH script 20190923_pgen_fastp_EPI_trimming.sh.

- 20190923_pgen_fastp_EPI_trimming.sh: SBATCH script to run fastp trimming.

- *fastqc.html: HTML files generated by FastQC analysis, post-trimming.

- *fastqc.zip: ZIP files of FastQC output, post-trimming.

- *20bp-trim.fq.gz: Trimmed FastQ files. The first 20bp from the 5' end of each read was trimmed.

- fastp.html: HTML report generated by fastp.

- fastp.json: JSON report generated by fastp.

- fastq.list.txt: List of the FastQ files processed.

- multiqc_data: Directory containing MultiQC analysis data. Data is summarized in the multiqc_report.html file.

- multiqc_report.html: HTML summary report of fastp and FastQC analyses, post-trimming.

- slurm-1347715.out: Mox SLURM output file containing stderr/stdout from fastp.

- system_path.log: Contents of Sam's system PATH on Mox.


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Notebook:

https://robertslab.github.io/sams-notebook/2019/09/23/TrimmingFastqcMultiQC-P.generosa-EPI-FastQs-with-FASTP-on-Mox.html