Please add this screenshot also in my previous query.Can I join this
contigs?
On 7 October 2015 at 10:10, Rameez Mj <rameez03online@xxxxxxxxx> wrote:
Thank you very much Hoefler and Chevreux for helping .Now I am getting the
colour assisted hash tags.
On 7 October 2015 at 09:59, Rameez Mj <rameez03online@xxxxxxxxx> wrote:
Ok Thank you Chevreux for the explanation. I will try this. I started
using gap5 to find internal joints. How to decide if I join two contigs or
not. I am attaching some screen shots please give me your suggestion about
joining in those cases. In case 4, one side of overlap is clean and
clear(case4.1) but other side of overlap is having so many
mismatches(case4.2). What I did in case 4 was split the contigs from where
the mismatch starts. In some cases of mismatches one consensus have low
base confidence(11) compared to other consensus(126) can I accept the base
from second consensus and join the contigs?. Please share your much valued
opinion and suggestion in this.
On 6 October 2015 at 19:53, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
On October 6, 2015 at 12:47 AM Rameez Mj <rameez03online@xxxxxxxxx>
wrote:
I made a gap5 database from CAF output file. But there is no colourtag
available in gap5.happening
All reads appear in a purple colour throughout the sequence. What is
should I invoke
mira to tag wile assebly separately?
You need to teach gap4/gap5 the tags MIRA is using. You will find a file
GTAGDB
in the "support" directory of MIRA. Append the content of this file to
the
GTAGDB file of the Staden gap4 or gap5 distribution you are using. For
gap5,
this file is located in
$STADENROOT/share/staden/etc
where $STADENROOT is the installation directory of your staden
distribution.
B.
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