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):

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:


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

from Sam’s Notebook https://ift.tt/2GpM7o2

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