Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Code Block
languagebash
cd 
ln -s -f $SCRATCH scratch
ln -s -f $WORK$WORK2 workwork2
ln -s -f /workwork2/projects/BioITeam

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /workwork2/projects/BioITeam/commonprojects/bincourses/launcher_maker.py
ln -s -f /work/projects/BioITeam/ls5/opt/cutadapt-1.10/bin/cutadaptCore_NGS_Tools CoreNGS

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /workwork2/projects/BioITeam/ls5common/opt/multiqc-1.0/multiqcbin/launcher_creator.py
ln -s -f /workwork2/projects/BioITeam/ls5common/opt/samstat-1.09/samstatbin/launcher_maker.py

Anchor
Catchup_bashrc
Catchup_bashrc
.bashrc setup

...

Code Block
languagebash
cd
cp .bashrc .bashrc.beforeNGSbeforeNGSTools

Copy and configure the login profile for this class

Code Block
languagebash
cd
cp /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5.stampede2  .bashrc
chmod 600 .bashrc

# or, using your symlink
cd
cp ~/CoreNGS/tacc/bashrc.corengs.stampede2  .bashrc
chmod 600 .bashrc

...

Code Block
languagebash
export ALLOCATION=UT-2015-05-18
export BI=/corral-repl/utexas/BioITeam
export BIWORK=/workwork2/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools

 exportexport PATH=.:$HOME/local/bin:$PATH
# For cutadapt support:
export PYTHONPATH=$BIWORK/ls5/lib/python2.7/site-packages:$PYTHONPATH
# For MultiQC support:
export PYTHONPATH=$BIWORK/ls5/lib/python2.7/annab-packages:$PYTHONPATH

Turn on coloring by file type in the shell:

Code Block
languagebash
export LS_OPTIONS='-N --color=auto -T 0'

# For better colors using a whitedark background terminal, un-comment this line:
export LS_COLORS=$LS_COLORS:'di=1;33:fi=01:ln=01;36:'

# For better colors using a white background terminal:
export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:'

# May or may not be needed
export LS_OPTIONS='-N --color=auto -T 0

TACC intro

Anchor
Catchup_cmds
Catchup_cmds
Commands files

...

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 .

...

Code Block
languagebash
titleStart an idev session
idev -p normal -m 180120 -N 1 -n 2468 -A UT-2015-05-18 --reservation=CCBBBIO_DATA_week_1
Tip

You can tell you're in a idev session because the hostname command will return a compute node name (e.g. nid00438. c401-041.stampede2.tacc.utexas.edu) instead of a login node name (e.g. login5 login2.stampede2.tacc.utexas.edu).

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

...

Working with some yeast ChIP-seq FASTQ data:

Code Block
languagebash
# AreaCreate fora "original"$SCRATCH sequencingarea datato mkdirwork -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
on data for this course,
# with a sub-direct[1ory for pre-processing raw fastq files
mkdir -p $SCRATCH/core_ngs/fastq_prep

# Make symbolic links to the original yeast data:
cd $SCRATCH/core_ngs/fastq_prep
ln -s -f $WORK/archive/original/2018_05.core_ngs$CORENGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
ln -s -f $WORK/archive/original/2018_05.core_ngs$CORENGS/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

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

...

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

...

Code Block
languagebash
# Pre-built references
mkdir -p $SCRATCH/core_ngs/references
rsync -ptlvrPavrP $CORENGS/references/ $SCRATCH/core_ngs/references/

# FASTQ (to align)
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/*fastq.gz $SCRATCH/core_ngs/alignment/fastq/

# Alignment directory
mkdir -p $SCRATCH/core_ngs/alignment/yeast_bwa
cd $SCRATCH/core_ngs/alignment/yeast_bwa
ln -s -f ../fastq
ln -s -f ../../references/bwa/sacCer3

module load biocontainers  # takes a while
module load bwa
module load samtools

Anchor
Catchup_bwa_pe_yeast
Catchup_bwa_pe_yeast
samtools manipulation of aligned yeast data

To jump into post-alignment manipulation of the yeast_pairedend.bam with samtools:

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/alignment/yeast_bwa
cd $SCRATCH/core_ngs/alignment/yeast_bwa
cp $CORENGS/catchup/yeast_bwa/yeast_pairedend.bam .

module load biocontainers  # takes a while
module load samtools

# If the sorted, indexed BAM is needed:
cp $CORENGS/catchup/yeast_bwa/yeast_pairedend.sort* .

SAMTools and BEDTools

Anchor
Catchup_samtools
Catchup_samtools
Setup for samtools

Code Block
languagebash
titleSetup for samtools exercises
mkdir -p $SCRATCH/core_ngs/samtools
cd $SCRATCH/core_ngs/samtools
cp $CORENGS/catchup/for_samtools/* .

module load biocontainers  # takes a while
module load samtools