A simple grep command solve your problem to extract the reads...If I am not
wrong you can save the unassembled reads in a file. Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
Microbial Biotechnology DepartmentFellow of http://obrasocial.lacaixa.es/
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El Martes 19 de Mayo de 2015 23:01, Adriana Fróes <dricamfroes@xxxxxxxxx>
escribió:
Yes, the same case as me. I have 3 reference plasmids. If you could send me
the python script, I'll appreciate a lot. my email is: dricamfroes@xxxxxxxxx
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 4:48 PM, Felipe Lira <felipelira3@xxxxxxxxxxxx> wrote:
I agree with Adrian, because without any reference MIRA will not be forced to
find your read position..
Good luck. Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
Microbial Biotechnology DepartmentFellow of http://obrasocial.lacaixa.es/
Antes de imprimir este mensaje piense bien si es realmente necesario
hacerlo.Before you print this e-mail, think well if it is really necessary.
El Martes 19 de Mayo de 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 plasmids and those
plasmids have similar sequences,
will the reads map in both plasmids or just in one of them.
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...)
