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


20180516 - UPDATE!!

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

WILL RE-RUN


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)(https://github.com/hputnam/project_juvenile_geoduck_OA/tree/master/Sample_Processing)

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)(https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20180514_roadrunner_geoduck_RRBS_trimming.ipynb)

Results:
TrimGalore! output folder:
FastQC output folder:
MultiQC output folder:
MultiQC report (HTML):