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Old 08-16-2018, 04:00 AM   #1
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Default cannot make sense of BWA MEM results, help!!

hi, been using both Bowtie2 and BWA mem with sequencing data from different species
Bowtie 2 results make sense, since I get a higher % of aligned reads when comparing to the species that is closer phylogenetically (50%) relative to other 2 species which are less related (25%)

However, when I use BWA mem, I get a higher but similar % of alignment with all 3 sp, around 85%. Much higher number of alignments but does not make sense from a phylogenetic point of view. I am using the default options in BWA mem.

Anyone have any thoughts? ideas? would be much appreciated
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