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The most important statistic is the mapping rate, but this readout allows you to verify that some common expectations (e.g. that about the same number of R1 and R2 reads aligned, and that most mapped reads are proper pairs) are met.

Exercise #6: Yeast BWA PE alignment with Anna's script

Now that you've done everything the hard way, let's see how to do run an alignment pipeline using Anna's script.

First the setup:

mkdir -p $SCRATCH/core_ngs/align2/fastq
cd $SCRATCH/core_ngs/align2/fastq
cp /corral-repl/utexas/BioITeam/core_ngs_tools/alignment/*fastq.gz .

Now change into the directory and call the script with no arguments to see usage

cd $SCRATCH/core_ngs/align2
/work/01063/abattenh/seq/code/script/align/align_bwa_illumina.sh