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Before the alignment, of course, we've got to build a mirbase index using bowtie2-build (go ahead and check out its options). Unlike for the aligner itself, we only need to worry about a few things here:

bowtie2-build <reference_in> <bt2_index_base>

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• reference_in file is just the FASTA file containing mirbase v20 sequences

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• bt2_index_base is the prefix of where we want the files to go

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 Following what we did earlier for BWA indexing:

mkdir -p $WORK/archive/references/bt2/mirbase.v20
cd $WORK/archive/references/bt2/mirbase.v20
ln -s -f ../../fasta/hairpin_cDNA_hsa.fa
ls mirbase
cd mirbase
-la

Now build the index with bowtie2-build:

bowtie2-build hairpin_cDNA_hsa.fa hairpin_cDNA_hsa.fa

That was very fast!  It's because the mirbase reference genome is so small compared to what programs like this are used to dealing with, which is the human genome (or bigger).  Now, your $SCRATCH/references/mirbase directory should be filled with   You should see the following files:

hairpin_cDNA_hsa.fa
hairpin_cDNA_hsa.fa.1.bt2
hairpin_cDNA_hsa.fa.2.bt2
hairpin_cDNA_hsa.fa.3.bt2
hairpin_cDNA_hsa.fa.4.bt2
hairpin_cDNA_hsa.fa.rev.1.bt2
hairpin_cDNA_hsa.fa.rev.2.bt2

Now, we're ready to actually try to do the alignment.  Remember, unlike BWA, we actually need to set some options depending on what we're after.  These are Some of the most important options when using Bowtie2for bowtie2 are:

To decide how we want to go about doing our alignment, check out the file we're aligning with 'less'.:

cds
less fastq_align/human_mirnaseq.fastq.gz

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