--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left date: 2018-04-09 23:25:01+00:00 layout: post slug: trimgalorefastqcmultiqc-auto-trim-c-virginica-mbd-bs-seq-fastq-data title: TrimGalore/FastQC/MultiQC - Auto-trim C.virginica MBD BS-seq FASTQ data categories: - 2018 - Miscellaneous tags: - Crassostrea virginica - Eastern oyster - FASTQC - MBD-Seq - multiqc - TrimGalore! --- [Yesterday, I ran FastQC/MultiQC on the _Crassostrea virginica_ MBD BS-seq data from ZymoResearch](https://robertslab.github.io/sams-notebook/posts/2018/2018-04-09-fastqcmultiqc-c-virginica-mbd-bs-seq-data/). Steven wanted to trim it and see how things turned out. I ran TrimGalore (using the built-in FastQC option) and followed up with MultiQC for a summary of the FastQC reports. TrimGalore job script: * [20180409_trimgalore_autotrim_Cvirginica_MBD.sh](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_trimgalore_autotrim_Cvirginica_MBD.sh) Standard error was redirected on the command line to this file: * [20180409_trimgalore_autotrim_Cvirginica_MBD/stderr.log](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/stderr.log) MD5 checksums were generated on the resulting trimmed FASTQ files: * [20180409_trimgalore_autotrim_Cvirginica_MBD/checksums.md5](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/checksums.md5) All data was copied to my folder on Owl. Checksums for FASTQ files were verified post-data transfer. ##### Results: Output folder: * [20180409_trimgalore_autotrim_Cvirginica_MBD/](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/) FastQC output folder: * [20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD/](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD/) MultiQC output folder: * [20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD/multiqc_data/](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD/multiqc_data/) MultiQC HTML report: * [20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD/multiqc_data/multiqc_report.html](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD/multiqc_data/multiqc_report.html) Overall, the auto-trim didn't alter things too much. Specifically, Steven is concerned about the variability in the first 15bp ([seen in the Per Base Sequence Content section of the MultiQC output](https://owl.fish.washington.edu/Athaliana/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD/multiqc_data/multiqc_report.html#fastqc_per_base_sequence_content)). It was reduced, but not greatly. Will perform an independent run of TrimGalore and employ a hard trim of the first 14bp of each read and see how that looks.