This is an interesting doubt. I'm trying something similar. I tried to use
MIRA with the option to keep the unassembled sequences, but I didn't find
the file with the unassembled. Do you know?
thanks
Adriana M. Froes
Laboratório de Microbiologia, Instituto de Biologia, Depto de Biologia
Marinha
Universidade Federal do Rio de Janeiro
Av. Carlos Chagas Filho 373, Sala A3-202, Bloco A (Anexo) do CCS
21941-599, Ilha do Fundão, Rio de Janeiro, RJ
On Tue, May 19, 2015 at 10:37 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>
wrote:
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 andthose
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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