Roberto’s Noreboock: FastQC of libraries with additional WGBS.

The results seems like before, with low Qval at the last positions.
Example of library 0501_R1_001_fastq.gz
/home/roberto/Pictures/Screenshot from 2019-05-03 14-31-08.png

Using this data, Trimming is running with conditions:
java -jar /home/Apps/trimmomatic/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 /home/Data_MeOH/Seq_data/0501_R1_001.fastq.gz /home/Data_MeOH/Seq_data/0501_R2_001.fastq.gz 0501_R1_001_paired.fastq.gz 0501_R1_001_unpaired.fastq.gz 0501_R2_001_paired.fastq.gz 0501_R2_001_unpaired.fastq.gz ILLUMINACLIP:TrueSeq3-PE.fa:2:30:10 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:20

I did not consider the min-length option. Last time, considering MINLENGTH:100 was not good. It reduces from 58 million of reads to 35 million…

fastQC before trimming (this library has not the Additional 25% of Seqs)
/home/roberto/Pictures/Screenshot from 2019-05-03 14-37-56.png

After trimming, the result was:
/home/roberto/Pictures/Screenshot from 2019-05-03 14-40-04.png

For this reason, the MINLENGTH is not used.

Laura’s Notebook: May 2019 Goals

Accomplished last couple months:

  • O. lurida 2017-2018 project (OA/Temp carryover)
    • Revised O. lurida 2017 manuscript
    • Sent O. lurida 2017 manuscript to co-authors for review
  • O. lurida 2018 project (Temp/Food carryover)
    • Analyzed data
    • Drafted methods and results section
    • Began drafting Discussion
  • Polydora paper
    • Revised based on Brady’s feedback, sent back to Brady
  • Helped/facilitated Alanna with RNA extractions
  • Finished FSH 324 TA-ship/grading
  • Began FSH 310 TA-ship
  • Revised Multivariate Stats class paper for “publication” in EJAMS
  • Odds and ends

Goals / To-Do list:

  • O. lurida 2017-2018 project (OA/Temp carryover)
    • Revise O. lurida 2017-2018 MS co-author feedback
  • O. lurida 2018 project (Temp/Food carryover)
    • Finish Discussion
    • Write Intro
    • Finalize plots
    • Send to co-authors
  • Bypass:
    • Write and submit bypass!
  • NSF GRFP
    • Meet with Krista N. re: NSF GRFP
    • Confirm that I’ll take my final NSF GRFP funding next year, and submit to NSF
  • Oly methylation data:
    • Pull matrices for Katherine
    • Wrap my head around action plan
  • Oly QuantSeq data:
    • Revisit – plan of attack. Do I want to do some juvenile Port Gamble whole-body samples to compare those with high pCO2 parental histories vs. no history, in the location where parental history correlated with survival?
    • Start testing QuantSeq analysis pipeline with Oly genome, Salmon (removing the multiple read/transcript auto-correct), Trinity’s isogroup designation file.

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