Update file qc_exercise.md

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
+