Steven found out that the Bismarck documentation (Bismarck is the bisulfite aligner we use in our BS-seq pipeline) suggests trimming 10bp from both the 5′ and 3′ ends. Since this is the next step in our pipeline, we figured we should probably just follow their recommendations!
TrimGalore job script:
Standard error was redirected on the command line to this file:
MD5 checksums were generated on the resulting trimmed FASTQ files:
All data was copied to my folder on Owl.
Checksums for FASTQ files were verified post-data transfer (data not shown).
FastQC output folder:
MultiQC output folder:
MultiQC HTML report:
Hey! Look at that! Everything is much better! Thanks for the excellent documentation and suggestions, Bismarck!