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Quality Trim Chris's Mytilus BS data #2004

Closed sr320 closed 1 week ago

kubu4 commented 2 weeks ago

This is complete. Currently in process of rsync-ing to Gannet.

If you want to start working with trimmed reads on Klone, they're here:

/gscratch/scrubbed/samwhite/gitrepos/project-mytilus-methylation/output/00.10-trimming-fastp-FastQC-MultiQC/trimmed-fastqs

ChrisMantegna commented 2 weeks ago

Hey Y'all!

I just opened an issue re: these sequences not looking back to see that I am late to my own party! Moving my questions here since they apply.

  1. Looking at Sam's notebook for the process/ parameters for doing so - looks like FastQC and MultiQC should be run. Is that correct or am I missing a QC step?
  2. What would indicate a sequencer error?

Thanks! Chris

kubu4 commented 2 weeks ago

Look in this repo for more info:

https://github.com/RobertsLab/project-mytilus-methylation

Take a look at the multic_report.html file for the raw reads and see what you think. It's okay not to fully understand all the info in there.