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Add comprehensive sequencing project metadata table and results summary to README#7

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Add comprehensive sequencing project metadata table and results summary to README#7
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Copilot AI commented Oct 5, 2025 •
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Overview

This PR adds a comprehensive "Sequencing Project Summary" section to the README that documents all sequencing projects associated with the Pacific cod temperature study, along with a summary of key results to date.

Changes

New Sequencing Project Summary Table

Added a detailed metadata table covering all 7 sequencing projects in this study:

Project Type Samples Files Status
30-943133806 RNA-seq 80 160 Complete - 4,105 DEGs identified
H202SC23041287 lcWGS 157 314* Complete - WGSassign analysis
30-1149633765 WGS 350 700 In progress - heatwave genetics
30-1149634506 WGS 16 32 In progress - ecotype pilot
AN00025267 BS-seq 32 64 In progress - methylseq pipeline
AN00025268 BS-seq 32 64 Planned
30-1067895835 - 1 2 Planned

The table includes:

  • Project IDs and sequencing types
  • Accurate sample and file counts verified against MultiQC reports and analysis files
  • Naming schema patterns with real examples from the data
  • Current analysis status and key outcomes

Key Results Summary

Added a "Key Results to Date" section highlighting major findings:

  • RNA-seq differential expression: 4,105 DEGs between 9°C and 16°C treatments (padj < 0.05)
  • Gene ontology enrichment: Completed using DAVID
  • Population genetics: WGSassign analysis for spawning population assignment
  • Growth and physiology: Treatment effects on growth rates and condition indices
  • Methylation landscape: Genome-wide analysis in progress

Data Verification

All metadata was verified against repository files:

  • RNA-seq counts from output/05-cod-RNAseq-trimming/raw-fastqc/multiqc_data_2/multiqc_fastqc.txt
  • lcWGS counts from lcWGS/analysis-20240606/experimental/pcod-exp_filtered_bamslist.txt
  • DEG results from code/07-cod-RNAseq-DESeq2.md
  • Methylation samples from code/17.samplesheet.csv
  • Project descriptions from existing README and data files

This provides researchers with a clear, comprehensive overview of all sequencing efforts and their current status in investigating thermal stress responses in juvenile Pacific cod.

Fixes #[issue_number]

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Original prompt

This section details on the original issue you should resolve

<issue_title>Determine metadata on cod sequence files</issue_title>
<issue_description>Based on content of this repo including files in report directory - create a revised version of this table for the readme file such that a brief summary of the project is provided and any putative results to date.

Project Attributes

Project Unique samples FASTQ/FQ files Naming schema Examples
30-1067895835 1 2 SAMPLE_R{1,2}_001.fastq.gz 1D11_R1_001.fastq.gz, 1D11_R2_001.fastq.gz
30-1149633765 350 700 EXP###_R{1,2}_001.fastq.gz, MHW###_R{1,2}_001.fastq.gz EXP001_R1_001.fastq.gz, EXP001_R2_001.fastq.gz
30-1149634506 16 32 ET##_R{1,2}_001.fastq.gz ET22_R1_001.fastq.gz, ET22_R2_001.fastq.gz
30-943133806 80 260 NN[_SUFFIX]_R{1,2}_001.fastq.gz, RESUB-###_R{1,2}_001.fastq.gz 100_R1_001.fastq.gz, 100_R2_001.fastq.gz
AN00025267 32 64 ##B_{1,2}.fastq.gz (paired reads as _1/_2) 01B_1.fastq.gz, 01B_2.fastq.gz
AN00025268 32 64 ##B_{1,2}.fastq.gz (paired reads as _1/_2) 01B_1.fastq.gz, 01B_2.fastq.gz
H202SC23041287 157 356 GM##_*_{1,2}.fq.gz (sample GM##, multiple lanes/runs) GM1_CKDN230011839-1A_H5NNGDSX7_L1_1.fq.gz, GM1_CKDN230011839-1A_H5NNGDSX7_L1_2.fq.gz

Comments on the Issue (you are @copilot in this section)

Fixes #6

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@sr320
Add comprehensive sequencing project metadata table and results summa…
050dfd2 
…ry to README

Co-authored-by: sr320 <4442039+sr320@users.noreply.github.com>
Copilot AI changed the title [WIP] Determine metadata on cod sequence files Add comprehensive sequencing project metadata table and results summary to README Oct 5, 2025
Copilot AI requested a review from sr320 October 5, 2025 18:17
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Determine metadata on cod sequence files

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