[mira_talk] Re: Mapping with more than one reference
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 2 Feb 2016 22:20:11 -0500
On 02 Feb 2016, at 8:35 , Roberta Rezende <rob.androida@xxxxxxxxx> wrote:
I’d like to know if I can map my reads against two or three genome references
ate the same time?
if yes I just duplicate my readgroup, like.. […]
Interesting question. To be truthful: I don’t know, that idea never came to me.
However, what I do know is that I presently cannot find a scenario where this
approach would be beneficial. On the contrary, everything I first thought of
had negative effects. E.g. what happens if NC_0001 and 0002 share an identical
stretch of genome, bchoc01 has it but bchoc02 not? Reads of bchoc02 would be
mapped to both NC0001 and 0002. With a lower coverage, but at first glance
algorithms would probably see nothing suspicious. Similar problematic for SNPs
between all four strains involved.
In short: even it were possible, I wouldn’t do it.
What are you actually trying to accomplish?
B.
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