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 referencesInteresting question. To be truthful: I don’t know, that idea never came to me.
ate the same time?
if yes I just duplicate my readgroup, like.. […]
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.