TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data

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20180516 - UPDATE!!

THIS WAS RUN WITH THE INCORRECT SETTING IN TRIMGALORE! --non-directional

WILL RE-RUN

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Steven requested that I trim the Geoduck RRBS libraries that we have, in preparation to run them through Bismark.

These libraries were originally created by Hollie Putnam using the TruSeq DNA Methylation Kit (Illumina):

• project_juvenile_geoduck_OA/Sample_Processing (GitHub)

All analysis is documented in a Jupyter Notebook; see link below.

Overview of process:

1. Copy EPI* FastQ files from owl/P_generosa to roadrunner.

2. Confirm data integrity via MD5 checksums.

3. Run TrimGalore! with --paired, --rrbs, and --non-directional settings.

4. Run FastQC and MultiQC on trimmed files.

5. Copy all data to owl (see Results below for link).

6. Confirm data integrity via MD5 checksums.

Jupyter Notebook:

• 20180514_roadrunner_geoduck_RRBS_trimming.ipynb (GitHub)

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Results:

TrimGalore! output folder:

• 20180514_geoduck_trimgalore_rrbs

FastQC output folder:

• 20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc/

MultiQC output folder:

• 20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc/multiqc_data

MultiQC report (HTML):

• multiqc_report.html