I already did this optionbut the problem is that I was not able to clearly
distinguish which plasmid I obtained. I thought with this option the
analysis could improve and determine which of the plasmid is the correct
one.
El 19/05/2015 18:47, "Adrian Pelin" <apelin20@xxxxxxxxx> escribió:
This may be silly of me to ask, but why not try a denovo accurate assembly
of your reads, and then match your contigs to the reference
genome/plasmids. This way you do not give MIRA any prior info on your data,
but instead you can compare the assembled results to what is known.
On Tue, May 19, 2015 at 12:43 PM, Dietmar Fernandez <
dietmar.fernandez@xxxxxxxxxxxx> wrote:
You can find the unasembled reads at de debrislist in the info? folder.
To select the reads ( no overlap and not align..) I develop a small python
script I could send you if you want and afterwards you could filter them
from the original fastq file (there is another script i don't remember
right now google??) in order to perform a de novo assembly with those reads
if you want.
El 19/05/2015 18:30, "Adriana Fróes" <dricamfroes@xxxxxxxxx> escribió:
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 plasmidsand 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 toput as
reference some plasmids and the one which is betterthe
represented will be the one that is present (taking into account all
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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