We decided to try improving things by running them through TrimGalore! to remove adapters and poor quality sequences.
Processed the samples on Roadrunner (Apple Xserve; Ubuntu 16.04) using default TrimGalore! settings.
After trimming, TrimGalore! output was summarized using MultiQC. Trimmed FastQ files were then analyzed with FastQC and followed up with MultiQC.
Documented in Jupyter Notebook (see below).
Jupyter Notebook (GitHub):
TrimGalore! output folder:
TrimGalore! MultiQC report (HTML):
TrimGalore! FastQC output folder:
FastQC MultiQC report (HTML:
Overall, things look a bit better, but there are still some issues. Will likely eliminate sample
2112_lane_1_TGACCA from analysis and apply some additional sequence filtering, based on sequence length.
SEQUENCE CONTENT PLOT
SHORT SEQUENCE CONTAMINATION