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

Now we're going to switch over to a different aligner that was originally designed for very short reads, and is frequently used for RNA-seq data.  Accordingly, we have prepared a test microRNA-seq dataset for you to experiment with.  This data is derived from a human H1 embryonic stem cell (H1-hESC) small RNA dataset generated by the ENCODE Consortium (its about a half million reads).  However, there is a problem!  We don't know (or, well, you don't know) what the adapter structure or sequences were.  So, you have a bunch of 36 base pair reads, but many of those reads will include extra sequence that will impede alignment!  We need an aligner that can find subsections of the read that align, and discard (or "soft-clip") the rest away.  Bowtie2 is just such an aligner.  Go ahead and load it up so we can examine some help pages and options.  To do that, you must first load the "perl" module, and then the bowtie2 module designated "bowtie/2.2.0". 

module load perl
module load bowtie/2.2.0
bowtie2

Now that it's loaded, 

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

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