diff --git a/exercises/qc_exercise.md b/exercises/qc_exercise.md index c97ee87facba17810393ea937cda39687ee0db49..1f71c463c4220c944f4ee15f25cd25b82397e166 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 +