Page Comparison

...

First prepare a directory to work infor the vibCho fasta, and change to it:

mkdir -p $SCRATCH/core_ngs/references/vibChofasta
cd $SCRATCH/core_ngs/references/vibChofasta

V. cholerae has two chromosomes. We download each separately.

...

mkdir -p $SCRATCH/core_ngs/references/vibChofasta
cd $SCRATCH/core_ngs/references/vibChofasta
cp $CORENGS/ncbireferences/vibChofasta/NC_* .

Once you have the 4 files locally in your $SCRATCH/core_ngs/references/vibCho directory, combine them using cat:

cd $SCRATCH/core_ngs/references/vibChofasta
cat NC_01258[23].fa   > vibCho.O395.fa
cat NC_01258[23].gff3 > vibCho.O395.gff3

# verify there are 2 contigs in vibCho.O395.fa
grep -P '^>' vibCho.O395.fa

Now we have a reference sequence file that we can use with the bowtie2 reference builder, and ultimately align sequence data against.

...

First create a directory specifically for the bowtie2 index, then build the index using bowtie-build.

mkdir -p $SCRATCH/core_ngs/references/

fasta
cd $SCRATCH/core_ngs/references/fasta
cp $CORENGS/references/

fasta/vibCho

* .

mkdir -p $SCRATCH/core_ngs/references/bt2/vibCho
cd $SCRATCH/core_ngs/references/bt2/vibCho.O395.fa

# or,Symlink to catch up: the fasta file you created using relative path syntax
ln -sf $CORENGS/references../../fasta/vibCho.O395.fa

bowtie2-build vibCho.O395.fa vibCho.O395

...

Performing the bowtie2 alignment

We'll set up a new Make sure you're in an idev session with the bowtie2 BioContainers module loaded:

idev -m 120 -A OTH21164  -N 1 -r CoreNGSday4
module load biocontainers
module load bowtie2

We'll set up a new directory to perform the V. cholerae data alignment. But first make sure you have the FASTQ file to align and the vibCho bowtie2 index:.

# Get the FASTQ to align a pre-built vibCho index if you didn't already build one
mkdir -p $SCRATCH/core_ngs/references/alignmentbt2/fastqvibCho
cp $CORENGS/references/bt2/alignmentvibCho/*fastq.gz*  $SCRATCH/core_ngs/references/alignmentbt2/fastqvibCho/

# SetGet upthe theFASTQ bowtie2to indexalign
mkdir -p $SCRATCH/core_ngs/referencesalignment/bt2/vibChofastq
cp $CORENGS/idx/bt2/vibChoalignment/*fastq.*gz  $SCRATCH/core_ngs/referencesalignment/bt2/vibCho/

Make sure you're in an idev session with the bowtie2 BioContainers module loaded:

idev -m 120 -A OTH21164  -N 1 -r CoreNGSday4
module load biocontainers
module load bowtie2fastq/

Now set up a directory to do this alignment, with symbolic links to the bowtie2 index directory and the directory containing the FASTQ to align:

...

So execute this bowtie2 global, single-end alignment command:

mkdir -p $SCRATCH/core_ngs/references/fasta
cp $CORENGS/references/fasta/vibCho*  $SCRATCH/core_ngs/references/fasta/

mkdir -p $SCRATCH/core_ngs/references/bt2/vibCho
cp $CORENGS/references/bt2/vibCho/*.*  $SCRATCH/core_ngs/references/bt2/vibCho/

mkdir -p $SCRATCH/core_ngs/alignment/vibCho
cd $SCRATCH/core_ngs/alignment/vibCho
ln -sf ../../references/bt2/vibCho
ln -sf ../../alignment/fastq fqmkdir -p $SCRATCH/core_ngs/alignment/vibCho

cd $SCRATCH/core_ngs/alignment/vibCho
bowtie2 -x vibCho/vibCho.O395 -U fq/cholera_rnaseq.fastq.gz -S cholera_rnaseq.sam 2>&1 | tee aln_global.log

...