Objectives
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BWA (the Burrows-Wheeler Aligner) is a fast short read aligner. It is an unspliced mapper. It's the successor to another aligner you might have used or heard of called MAQ (Mapping and Assembly with Quality). As the name suggests, it uses the burrows-wheeler transform to perform alignment in a time and memory efficient manner.
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ls ../data ls ../reference #transcriptome head ../reference/transcripts.fasta #see how many transcripts there are in the file grep -c '^>' ../reference/transcripts.fasta #genome head ../reference/genome.fa #see how many sequences there are in the file grep -c '^>' ../reference/genome.fa #annotation head ../reference/genes.formatted.gtf #see how many entries there are in this file wc -l ../reference/genes.formatted.gtf |
Load the module:Run BWA
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module load bwa |
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