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 colour taghappening
available in gap5.
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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