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:

• 20180410_trimgalore_trim14bp_Cvirginica_MDB.sh

Standard error was redirected on the command line to this file:

• 20180411_trimgalore_10bp_Cvirginica_MBD/stderr.log

MD5 checksums were generated on the resulting trimmed FASTQ files:

• 20180411_trimgalore_10bp_Cvirginica_MBD/checksums.md5

All data was copied to my folder on Owl.

Checksums for FASTQ files were verified post-data transfer (data not shown).

Results:

Output folder:

• 20180411_trimgalore_10bp_Cvirginica_MBD

FastQC output folder:

• 20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD

MultiQC output folder:

• 20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD/multiqc_data/

MultiQC HTML report:

• 20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD/multiqc_data/multiqc_report.html

Hey! Look at that! Everything is much better! Thanks for the excellent documentation and suggestions, Bismarck!