Question: BWA-MEM Syntax Understanding
0
gravatar for ggman
17 months ago by
ggman80
United States
ggman80 wrote:

Hey all,

I am trying to switch over from bowtie to BWA. There are many options that I don't understand once you attempt to align reads to the reference genome. Would it be better to leave these options as default, especially when it comes to the scoring?

GG

alignment bwa-mem • 439 views
ADD COMMENTlink modified 17 months ago by Devon Ryan94k • written 17 months ago by ggman80
2
gravatar for Devon Ryan
17 months ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

It's always best to use the defaults when you're first using a new program unless you're already familiar with their implications. That's true for every program you will ever use.

ADD COMMENTlink written 17 months ago by Devon Ryan94k

Gotcha, thanks Devon!

ADD REPLYlink written 17 months ago by ggman80
1

On top of that, you'll probably have a hard time even finding publications that use it with something other than the defaults, unless the task is something like matching synthetic reporter libraries with intentional small mutations in massively parallel reporter assays.

ADD REPLYlink written 17 months ago by ATpoint32k
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