Hello all
Recently we upgraded our miseq and got 2*250 run data. Does anyone have experience in aligning this sort of data? I have been using bwa till now for previous runs when it produced 2*150. Unable use bwa on this data using Bwasw as it didnot support paired end data. I am looking in to bowtie2 now to use as aligner. My references are amplicons and the size is approximately 2kb. In bowtie2, they are suggesting to use bowtie2 for longer genomes. Any thoughts on this?
Recently we upgraded our miseq and got 2*250 run data. Does anyone have experience in aligning this sort of data? I have been using bwa till now for previous runs when it produced 2*150. Unable use bwa on this data using Bwasw as it didnot support paired end data. I am looking in to bowtie2 now to use as aligner. My references are amplicons and the size is approximately 2kb. In bowtie2, they are suggesting to use bowtie2 for longer genomes. Any thoughts on this?
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