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Copy and configure the login profile for this class

Code Block
languagebash
titleCopy a pre-configured login script
cd
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5  .bashrc
chmod 600 .bashrc

...

Code Block
languagebash
titleCopy a pre-configured login script
source ~/.bashrc

TACC intro

Anchor
Catchup_cmds
Catchup_cmds
Commands files

Simple commands

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/slurm/simple
cd $SCRATCH/core_ngs/slurm/simple
cp $CORENGS/tacc/simple.cmds

Wayness commands

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/slurm/wayness
cd $SCRATCH/core_ngs/slurm/wayness
cp $CORENGS/tacc/wayness.cmds .

Anchor
Catchup_idev
Catchup_idev
Start an idev session

To start an idev (interactive development) session:

...

The n idev session will terminate when the requested time has expired, or you use the exit command.

Working with FASTQ

Anchor
Catchup_yeast_data
Catchup_yeast_data
Yeast data

Working with some yeast ChIP-seq FASTQ data:

Code Block
languagebash
# Area for "original" sequencing data
mkdir -p $WORK/archive/original/2018_05.core_ngs
cd $WORK/archive/original/2018_05.core_ngs
wget http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
wget http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

# Create a $SCRATCH area for FASTQ prep and link the yeast data there
mkdir -p $SCRATCH/core_ngs/fastq_prep
cd $SCRATCH/core_ngs/fastq_prep
ln -s -f $WORK/archive/original/2018_05.core_ngs/Sample_Yeast_L005_R1.cat.fastq.gz
ln -s -f $WORK/archive/original/2018_05.core_ngs/Sample_Yeast_L005_R2.cat.fastq.gz

# Copy over a small FASTQ file
cd $SCRATCH/core_ngs/fastq_prep
cp $CORENGS/misc/small.fq .

Anchor
Catchup_multiqc
Catchup_multiqc
ATACseq data for MultiQC

Get some FastQC reports for MultiQC:

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/multiqc/fqc.atacseq
cd $SCRATCH/core_ngs/multiqc/fqc.atacseq
cp $CORENGS/multiqc/fqc.atacseq/*.html

Anchor
Catchup_cutadapt
Catchup_cutadapt
FASTQ files for cutadapt

For command-line cutadapt exploration:

Code Block
languagebash
cd $SCRATCH/core_ngs/fastq_prep
cp $CORENGS/human_stuff/Sample_H54_miRNA_L004_R1.cat.fastq.gz .
cp $CORENGS/human_stuff/Sample_H54_miRNA_L005_R1.cat.fastq.gz .
zcat Sample_H54_miRNA_L004_R1.cat.fastq.gz | head -2000 > miRNA_test.fq

For batch cutadapt processing:

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/cutadapt
cd $SCRATCH/core_ngs/cutadapt
cp $CORENGS/human_stuff/Sample_H54_miRNA_L004_R1.cat.fastq.gz .
cp $CORENGS/human_stuff/Sample_H54_miRNA_L005_R1.cat.fastq.gz .
cp $CORENGS/yeast_stuff/Yeast_RNAseq_L002_R1.fastq.gz .
cp $CORENGS/yeast_stuff/Yeast_RNAseq_L002_R2.fastq.gz .
cp $CORENGS/tacc/cuta.cmds .

Alignment workflow

Setup

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