From bef6d4b07d3c695f940b89a92ac7b3d4bde6274d Mon Sep 17 00:00:00 2001
From: Srinithi Purushothaman <spurushothaman@imm.uzh.ch>
Date: Tue, 19 Mar 2024 14:32:53 +0100
Subject: [PATCH] Update file qc_exercise.md

---
 exercises/qc_exercise.md | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/exercises/qc_exercise.md b/exercises/qc_exercise.md
index c97ee87..1f71c46 100644
--- a/exercises/qc_exercise.md
+++ b/exercises/qc_exercise.md
@@ -2,12 +2,24 @@
 
 This document has the path for the sequencing summary files to be copied for the exercises.
 
-## Absolute path for sequencing summary files
+## Absolute path for nanopore sequencing summary files
 
 `/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2024/Participants_data/nanopore/GroupA_upec/sequencing_summary_FAW69650_79a286a3_8781c1d7.txt` - seq summary file for upec qc
 
 `/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2024/Participants_data/nanopore/GroupB_mrsa/sequencing_summary_FAV81714_2608efeb_092333a0.txt` - seq summary file for mrsa qc
 
-## Path for QC script
+## Path for nanopore QC script
 
 `/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2024/Participants_data/nanopore_scripts/nanopore_qc_nanoplot.sh` - Nanoplot script 
+
+## Path for illumina data
+
+`/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2024/Participants_data/illumina/01_data_mrsa/` - raw fastq files for mrsa
+
+`/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2024/Participants_data/illumina/01_data_upec/` - raw fastq files for upec
+
+## Path for illumina QC script
+`/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2024/Participants_data/illumina/02_scripts/fastqc_mrsa.sh` - fastqc script for mrsa
+
+`/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2024/Participants_data/illumina/02_scripts/fastqc_upec.sh` - fastqc script for upec
+
-- 
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