[mira_talk] Re: De novo assemblie. Reference genome and plasmids genomes?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 19 May 2015 16:37:15 +0200 (CEST)
On May 19, 2015 at 4:17 PM Dietmar Fernandez <dietmar.fernandez@xxxxxxxxxxxx>
wrote:
1) Another question is that if two of the references are plasmids and those
plasmids have similar sequences,
will the reads map in both plasmids or just in one of them.
Reads will always map to the best matching reference. Only if the potential
matches are 100% identical, reads will be distributed across the match sites.
2) In order to detect which plasmid is present, is it possible to put as
reference some plasmids and the one which is better
represented will be the one that is present (taking into account all the
plasmids have common sequences...)
You'll have to try it out, but bomething like that is probably the way to go.
You may want to make a trial where you throw out 100% identical sequences in all
plasmids though to maybe get a clearer signal.
B.
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