From b38808f668a54f986bff4ee222a2cf2e5d446f5f Mon Sep 17 00:00:00 2001 From: candicechu Date: Fri, 11 Mar 2016 16:03:10 -0600 Subject: [PATCH] Updated CTEHR Training (markdown) --- CTEHR-Training.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/CTEHR-Training.md b/CTEHR-Training.md index 3ac48f3..366e4b1 100644 --- a/CTEHR-Training.md +++ b/CTEHR-Training.md @@ -19,6 +19,5 @@ To verify that the pipeline is installed and up-to-date, navigate to the `sequen modifying the cut commmand on [this line](https://github.com/chapkinlab/sequencing-pipeline/blob/80061158cfebb1dda2c7806779b53466573cc337/main-scripts/concat.sh#L34) from 1-4 to 1-5 in `concat.sh`. remove the # commenting character) [this line](https://github.com/chapkinlab/sequencing-pipeline/blob/3155b43c4877023fc7a6b5699b77dd42d9bc2389/main-scripts/concat.sh#L50) in your local copy of the concat.sh script and then run it. `mkdir FastqFile_processed` -`./sequencing-pipeline/main-scripts/concat.sh ./FastqFile/ ./FastqFile_processed concat.sh_processed_list.txt` -FastqFile/Sample_DMSO1/DMSO1_AGTTCC_L001_R1_001.fastq.gz -FastqFile/Sample_DMSO1/DMSO1_AGTTCC_L002_R1_002.fastq.gz +`./sequencing-pipeline/main-scripts/concat.sh ./FastqFile/ ./FastqFile_processed` +