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You have already worked with a paired-end yeast ChIP-seq dataset, which we will continue to use here.  We  The paired end data should be located at:

$SCRATCH/YEAST_FASTQ_AFTER_DAY_2

We will also use two additional RNA-seq datasets.  The additional data , which are located in the pathat:

$SCRATCH/corral-repl/utexas/BioITeam/core_ngs_tools/human_stuff 

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stuff

Set up a new directory in your scratch area called 'fastq_align', and populate it with copies the following files, derived from the locations given above:

cds
mkdir fastq_align
cd fastq_align
cp $SCRATCH/YEAST_FASTQ_AFTER_DAY_2 /corral-repl/utexas/BioITeam/core_ngs_tools/human_stuff/*rnaseq.fastq.gz .

Do a fast quality check on the two new data files like you did earlier on the yeast files, and move all files and directories that are produced from the fastQC commands into a new subdirectory called 'fastqc_out'.

cd $SCRATCH/core_ngs_toolsfastq_align
mkdir fastqc_out
module load fastqc
fastqc human_rnaseq.fastq.gz
fastqc human_mirnaseq.fastq.gz
mv *fastqc* fastqc_out

Reference Genomes

Before we get to alignment, we need a genome to align to.  We will use three different references here:  the human genome (hg19), the yeast genome (sacCer3), and mirbase (v20).  Mirbase is a collection of all known microRNAs in all species, and we will use the human subset of that database as our alignment reference.  This has the advantage of being significantly smaller than the human genome, while containing all the sequences we are actually interested in.

These are the three reference genomes we will be using today, with some information about them (and here is information about many more genomes):

Searching genomes, however, is hard work and takes a long time if done on an un-indexed, linear genomic sequence.  So, most aligners require that references be indexed for quick access  The aligners we are using each require a different index, but use the same method (the Burrows-Wheeler Transform) to get the job done.  This requires taking a FASTA file as input, with each chromosome (or contig) as a separate entry, and producing some aligner-specific set of files as output.  Then, those output files are used by the aligner when executing a given alignment command. Here are some details of where you can find the references we need now (and here are many more):

The yeast and mirbase fasta files (with just reference sequence information) are located on the path:

/

Hg19 is way too big for us to index here, so we've already done it.  

 Hg19 is way too big for us to index here, so we're not going to do it, and it's not included in the core_ngs_tools directory at Corral that we've been copying from.  Instead, all hg19 index files are located at:

/scratch/01063/abattenh/ref_genome/bwa/bwtsw/hg19

Now, we're going to grab the other two references, and we will build each index right before we use it in each set of exercise below.  These two references are located at:

/corral-repl/utexas/BioITeam/core_ngs_tools/references/sacCer3.fa
/corral-repl/utexas/BioITeam/core_ngs_tools/references/hairpin_cDNA_hsa.fa

Now, stage the yeast and mirbase reference fasta files in your scratch area in a directory called 'references'.

cp -r /corral-repl/utexas/BioITeam/core_ngs_tools/references/*.fa $SCRATCH/

With that, we're ready to get started on the first exercise.

Exercise #1: BWA - Yeast ChIP-seq

Exercise #2: Bowtie2 and Local Alignment - Human microRNA-seq

Exercise #3: BWA-MEM (and Tophat2) - Human mRNA-seq

Future Directions