---
title: "RNAseq data FastQC and trimming"
author: "Kathleen Durkin"
date: "2024-03-04"
categories: ["pacifc-cod"]
format:
  html
---

Data recieved from Azenta Feb. 21, 2024 (project 30-943133806) (see [Sam's notebook post](https://robertslab.github.io/sams-notebook/posts/2024/2024-02-21-Data-Received---Pacific-cod-RNA-seq-Azenta-Project-30-943133806/)).

Evaluated raw read sequence quality using FastQC (and used MultiQC to visualize all reads simultaneously)

[Code](https://github.com/RobertsLab/project-cod-temperature/blob/main/code/05-cod-RNAseq-trimming.Rmd)\
[Rendered code](https://github.com/RobertsLab/project-cod-temperature/blob/main/code/05-cod-RNAseq-trimming.md)

Individual FastQC reports for each sequence are stored [here](https://gannet.fish.washington.edu/kdurkin1/C_macrocephalus/RNAseq/), and you can view the spreadsheet containing read-specific links and metadata [here](https://docs.google.com/spreadsheets/d/1_XqIOPVHSBVGscnjzDSWUeRL7HUHXfaHxVzec-I-8Xk/edit#gid=0).

### MultiQC Report Summary

Can view full MultiQC report [here](https://gannet.fish.washington.edu/kdurkin1/C_macrocephalus/RNAseq/multiqc_report.html)

![](images/fastqc-status-check-heatmap.png)

![](images/cod_multiqc_seqcount.png)

![](images/cod_multiqc_meanquality.png)

![](images/cod_multiqc_perseqquality.png)

![](images/cod_multiqc_persecGC.png)

![](images/cod_multiqc_overrepseq.png)

![](images/cod_multiqc_adapcontent-01.png)