Starting the process of working with summer 2022 Pycnopodia helianthoides coelomocyte RNAseq data. This will be part of my talk for SICB in January, and for WSN I’ll be focusing on presenting the work I have already done from summer 2021.
Summer 2022 Raw Data
The raw RNAseq data lives on owl: https://owl.fish.washington.edu/nightingales/P_helianthoides/
The data for summer 2022 are the files with the prefix “PSC-0”. Here’s a link to the google sheet with sample info (will put into github repo soon): here
Pre-trimming QC:
Following my protocol here: RNAseq-pipeline.md
Some adjustments to that specific protocol for summer 2022 data are:
2. Quality Check and Trimming
1. Untrimmed Data Quality Check Part I: FASTQC
Summer 2022 .fastq.gz files from Owl are on Raven in: /home/shared/8TB_HDD_02/graceac9/pycnornaseq2022
Multiqc report for untrimmed data on owl: owl.fish.washington.edu/scaphapoda/grace/pycno_2022/multiqc/mutliqc_report.html
3. Trim RNAseq data: Run fastp on Mox, then multiqc
A. rsync RNAseq data (fastq.gz) from nightingales to /gscratch/srlab/graceac9/data/pycno/RNAseq/summer2022
B. Script for summer 2022 will be in:
/gscratch/scrubbed/graceac9/jobs/20231101_pycno2022_fastp.sh
Trimmed data on Mox is: /gscratch/srlab/graceac9/analyses/pycno/20231101_PSC2022_trimming
Moved the trimmed data’s multiqc report to owl: owl.fish.washington.edu/scaphapoda/grace/pycno_2022/multiqc/trimmed/multiqc_report.html