From f2b19ed6a0151d91b0348a48d781f5ecfd30c517 Mon Sep 17 00:00:00 2001 From: Matt Bixley Date: Mon, 11 Mar 2024 10:34:10 +1300 Subject: [PATCH] Update 2_qualityassessment.md removes $ and combined code chunks --- docs/2_qualityassessment.md | 49 +++++++++++++------------------------ 1 file changed, 17 insertions(+), 32 deletions(-) diff --git a/docs/2_qualityassessment.md b/docs/2_qualityassessment.md index 5f9e852..5784b5f 100644 --- a/docs/2_qualityassessment.md +++ b/docs/2_qualityassessment.md @@ -21,8 +21,6 @@ First, it is always good to verify where we are: ```bash cd ~ -``` -```bash pwd ``` @@ -34,23 +32,24 @@ pwd Checking to make sure we have the Raw files for the workshop. ```bash -$ ls +ls +``` +```bash RNA_seq ... ``` Creating a directory where to store the QC data: ```bash -$ cd RNA_seq +cd RNA_seq +ls ``` - ```bash -$ ls Genome Raw rsmodules.sh yeast_counts_all_chr.txt ``` ```bash -$ mkdir QC +mkdir QC ``` Since we are working on the NeSI HPC, we need to search and load the software/application before we can use it. @@ -61,13 +60,13 @@ Since we are working on the NeSI HPC, we need to search and load the software/ap ```bash #View all modules - $ module avail + module avail # View all modules which match the keyword in their name - $ module avail KEYWORD + module avail KEYWORD # View all modules which match the keyword in their name or description - $ module spider KEYWORD + module spider KEYWORD ``` * Load a specific program @@ -75,21 +74,21 @@ Since we are working on the NeSI HPC, we need to search and load the software/ap >All module names on NeSI Software stack have a version and toolchain/environment suffixes. If none is specified, then the default version of the software is loaded. The default version can be seen with the `module avail modulename` command (corresponding module name will have `(D)` suffix) ```bash - $ module load Module_Name + module load Module_Name ``` * Unload all current modules ```bash - $ module purge + module purge ``` >Please **do not** use `$module --force purge` * Swap a currently loaded module for a different one ```bash - $ module switch CURRENT_MODULE DESIRED_MODULE + module switch CURRENT_MODULE DESIRED_MODULE ``` * Search whether the software is available as a module with `module spider` command. @@ -102,8 +101,6 @@ and then load ```bash module purge -``` -```bash module load FastQC/0.11.9 ``` @@ -138,7 +135,9 @@ Approx 35% complete for SRR014335-chr1.fastq The FastQC program has created several new files within our ***~/RNA_seq/QC/*** directory. ```bash -$ ls QC +ls QC +``` +```bash SRR014335-chr1_fastqc.html SRR014336-chr1_fastqc.zip SRR014339-chr1_fastqc.html SRR014340-chr1_fastqc.zip SRR014335-chr1_fastqc.zip SRR014337-chr1_fastqc.html SRR014339-chr1_fastqc.zip SRR014341-chr1_fastqc.html SRR014336-chr1_fastqc.html SRR014337-chr1_fastqc.zip SRR014340-chr1_fastqc.html SRR014341-chr1_fastqc.zip @@ -155,8 +154,6 @@ Now that we’ve looked at our HTML reports to get a feel for the data, let’s ```bash cd ~/RNA_seq/QC -``` -``` ls ``` ``` @@ -179,7 +176,7 @@ Inside each unzipped folder, there is a summary text which shows results of the ls SRR014335-chr1_fastqc ``` ``` - fastqc_data.txt fastqc.fo fastqc_report.html Icons/ Images/ summary.txt +fastqc_data.txt fastqc.fo fastqc_report.html Icons/ Images/ summary.txt ``` Use less to preview the summary.txt file @@ -209,23 +206,11 @@ cat */summary.txt > ~/RNA_seq/QC/fastqc_summaries.txt ```bash module load MultiQC/1.13-gimkl-2022a-Python-3.10.5 -``` -``` cd ~/RNA_seq/ -``` -``` mkdir MultiQC -``` -``` cd MultiQC -``` -``` cp ../QC/* ./ -``` -``` multiqc . -``` -``` ls -F ``` ```bash @@ -237,4 +222,4 @@ The html report shows the MultiQC summary - - - -

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