Hi would like to know how can I use bwa to align the reads using the standard aln method with the command:
and then use it again to align the unaligned reads with the dbwtsw Smith-Waterman-like alignment. Is there an easy way to extract from the .fastq+.sai files the list of reads that did not align?
bwa aln database.fasta short_read.fastq > aln_sa.sai
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