From 014b96e6e220b4c6cf12bb0fb1b3ce19355cdaeb Mon Sep 17 00:00:00 2001 From: Srinithi Purushothaman <spurushothaman@imm.uzh.ch> Date: Wed, 22 Mar 2023 12:50:09 +0100 Subject: [PATCH] added qc exercise --- exercises/qc_exercise.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 exercises/qc_exercise.md diff --git a/exercises/qc_exercise.md b/exercises/qc_exercise.md new file mode 100644 index 0000000..62be9ed --- /dev/null +++ b/exercises/qc_exercise.md @@ -0,0 +1,23 @@ +# Quality Control (QC) Exercises + +This document has the path for the sequencing data to be copied for the exercises. + +## Absolute path for raw data and files + +/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/01_data_mrsa - raw fastq files for mrsa from illumina + +/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/01_data_upec/ - raw fastq files for upec from illumina + +/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore/Group1_mrsa/rawdata_mrsa/ - raw fastq files for mrsa from nanopore + +/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore/Group2_upec/rawdata_upec/ - raw fastq files foe upec from nanopore + +/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore/Group1_mrsa/sequencing_summary_FAS74008_3919db7b_5086a1cb.txt - seq summary file for mrsa qc + +/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore/Group2_upec/sequencing_summary_FAS66307_6bec0f82_c8f87af5.txt - seq summary file for upec qc + +## Path for QC script + +/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore_scripts/nanopore_qc_nanoplot.sh + + -- GitLab