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idev -m 180120 -p normal -A UT-2015-05-18OTH21164 -N 1 -nr 68CoreNGSday4

Go ahead and load the bowtie2 module so we can examine some help pages and options.

module biocontainers
module load bowtiebowtie2

 Now that it's loaded, check out the options. There are a lot of them! In fact for the full range of options and their meaning, Google "Bowtie2 manual" and bring up that page (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml). The Table of Contents is several pages long! Ouch!

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

# Set up the bowtie2 index
mkdir -p $SCRATCH/core_ngs/references/bt2/vibCho
cp $CORENGS/idx/bt2/vibCho/*.*  $SCRATCH/core_ngs/references/bt2/vibCho

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

idev -p normal -m 120 -A UT-2015-05-18OTH21164  -N 1 -nr 68CoreNGSday4
module load biocontainers
module load bowtie

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

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We'll be aligning the V. cholerae reads now in ./fq/cholera_rnaseq.fastq.gz (how many sequences does it contain?)

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