[mira_talk] Re: Mapping with more than one reference

  • From: Dorina Lenz <dlenz@xxxxxxxxxxxxx>
  • To: <mira_talk@xxxxxxxxxxxxx>
  • Date: Wed, 3 Feb 2016 10:24:32 +0100

Hi,

if I want to map against more than one genome, I usually use a Multi-Fasta reference file.
In this case you just define one reference read group.

I usually do this if we are not sure which (sub-)species we sequenced, and to compare and choose the best reference available (for mitochondrial genomes).
But you could also choose the best reference if running a De-Novo assembly and blast your contigs.

Best,
Dorina


**
On 03/02/16 04:20, Bastien Chevreux wrote:

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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