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Go ahead and try to do a single-end alignment of the file to the human genome using bwa aln like we did in Exercise #1, saving intermediate files with the prefix human_rnaseq_bwa. Go ahead and just execute on the command line.
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bwa aln hg19/hg19.fa fq/human_rnaseq.fastq.gz > human_rnaseq_bwa.sai bwa samse hg19/hg19.fa human_rnaseq_bwa.sai fq/human_rnaseq.fastq.gz > human_rnaseq_bwa.sam |
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Because this file was generated exclusively from reads in a larger dataset that cross at least one splice junction. The sequences as they exists in most of the reads do not correspond to a single location in the genome. However subsections of each read do exist somewhere in the genome. So, we need an aligner that is capable aligning different parts of the read to different genomic loci. |
RNA-seq alignment with bwa mem
Exercise: use bwa mem to align the same data
Based on the following syntax and the above reference path, use bwa mem to align the same file, saving output files with the prefix human_rnaseq_mem. Go ahead and just execute on the command line.
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