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Updated CTEHR Training (markdown)
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candicechu committed Mar 11, 2016
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5 changes: 2 additions & 3 deletions CTEHR-Training.md
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Expand Up @@ -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`

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