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Code Block
languagebash
titlePrepare Bowtie2 index directory for mirbase
mkdir -p $WORK/core_ngs/references/bt2/mirbase.v20
mv $WORK/core_ngs/references/hairpin_cDNA_hsa.fa $WORK/core_ngs/references/fasta
cd $WORK/core_ngs/references/bt2/mirbase.v20
ln -s -f ../../fasta/hairpin_cDNA_hsa.fa
ls -la 
module load perl
module load bowtie/2.2.0

Now build the mirbase index with bowtie2-build like we did for the V. cholerae index:

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titleWhat's going on?
Code Block
languagebash
titleLocal bowti2 alignment of miRNA data
launcher_creator.py -n bt2 -j bt2.cmds -t 01:00:00 -A UT-2015-05-18
sbatch bt2.slurm; showq -u

#copy from Amelia's scratch:
cp /scratch/01786/awh394/core_ngs.test/alignment/human_mirnaseq.sam .

When the job is complete you should have a human_mirnaseq.sam file that you can examine using whatever commands you like. An example alignment looks like this.

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