I use a pipeline that uses bowtie as the aligner, however, due to genome size, I have had to alter this pipeline to use BWA. I need to run BWA in a way that will give me results equivalent as possible to how I run bowtie, but I am not entirely certain how to do this.
Here are the arguments we use in running bowtie:
-S -k 1 -m 1 --chunkmbs 3072 --best --strata -o 4 -e 80 -l 20 -n 0
Anyone have any suggestions on the best way to run BWA?
Here are the arguments we use in running bowtie:
-S -k 1 -m 1 --chunkmbs 3072 --best --strata -o 4 -e 80 -l 20 -n 0
Anyone have any suggestions on the best way to run BWA?
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