I. Concatenate newly trimmed reads

These newly trimmed reads are from analysis started on 8/6; see notebook entry here):

  • did this on mox:
    • copied data over from Ostrich/Gannet to Mox:

        rsync --archive --progress --verbose strigg@ostrich.fish.washington.edu:/Users/strigg/Desktop/Salmo_Calig/TRIM/*001_val_1.fq.gz /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/
        rsync --archive --progress --verbose strigg@ostrich.fish.washington.edu:/Users/strigg/Desktop/Salmo_Calig/TRIM/*001_val_2.fq.gz /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/

II. Run multiqc on newly trimmed reads

- copied data over from Ostrich/Gannet to Emu, ran multiQC, then copied back to Ostrich/Gannet:

srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ rsync --archive --progress --verbose strigg@ostrich.fish.washington.edu:/Users/strigg/Desktop/Salmo_Calig/TRIM/FASTQC .

srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc/FASTQC$ multiqc .
[INFO   ]         multiqc : This is MultiQC v0.9
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '.'

[INFO   ]          fastqc : Found 88 reports
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

rsync --archive --progress --verbose multiqc_data/ strigg@ostrich.fish.washington.edu:/Users/strigg/Desktop/Salmo_Calig/TRIM/FASTQC


III. Determine bismark parameters to apply

Sea lice:

For Salmon:

IV. Other options to consider

see suggestions from this article:

  • TrimGalore: retain unpaired
  • Bismark: PE save unmapped, then run bismark SE on unmapped reads

To investigate:

  1. How trimming affects mapping efficiency
  2. How many more mapped reads come from retaining unpaired trimmed reads + running Bismark SE on unmapped PE reads

I ran the following mox script on one Salmon sample (16C_26psu_1_S13):


  • run bamQC
    • BamQC outputs a lot of useful info including genome coverage and insert size
  • run full alignment with determined alignment parameters