Thank you Bastien!!
I do have in mind the quality file necesity and its benefits on the
assembly, but this is one of those* very rare occations* where no qualities
are available.
Best regards,
Pati
On Tue, Oct 6, 2015 at 11:10 PM, FreeLists Mailing List Manager <
ecartis@xxxxxxxxxxxxx> wrote:
mira_talk Digest Tue, 06 Oct 2015 Volume: 03 Issue: 112
In This Issue:
[mira_talk] Re: Not finding HAsh Frequency tag colours in
[mira_talk] Re: Assembling with no quality file. System
requ
[mira_talk] Re: Not finding HAsh Frequency tag colours in
[mira_talk] Re: Not finding HAsh Frequency tag colours in
[mira_talk] Re: Not finding HAsh Frequency tag colours in
[mira_talk] Re: Not finding HAsh Frequency tag colours in
[mira_talk] Re: Not finding HAsh Frequency tag colours in
[mira_talk] Re: Not finding HAsh Frequency tag colours in
----------------------------------------------------------------------
Date: Tue, 6 Oct 2015 09:16:38 -0500
Subject: [mira_talk] Re: Not finding HAsh Frequency tag colours in
From: Chris Hoefler <hoeflerb@xxxxxxxxx>
You need to update the gap5 tag file with the Mira tags.
cat {MIRA_PREFIX}/support/GTAGDB >> {STADEN_PREFIX}/share/staden/etc/GTAGDB
You will likely need administrator access to do this. Restart gap5 and you
should see all of the Mira tags.
On Mon, Oct 5, 2015 at 11:47 PM, Rameez Mj <rameez03online@xxxxxxxxx>
wrote:
I did an assembly with a manifest file which start like this
Project = 1247
Job = genome,denovo,accurate
parameters = -GE:not=4
parameters = -NW:cac=warn
I made a gap5 database from CAF output file. But there is no colour tag
available in gap5.All reads appear in a purple colour throughout the
sequence. What is happening should I invoke mira to tag wile assebly
separately?
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
------------------------------
Date: Tue, 6 Oct 2015 10:18:47 -0400 (EDT)
From: Bastien Chevreux <bach@xxxxxxxxxxxx>
Subject: [mira_talk] Re: Assembling with no quality file. System requesting
On October 6, 2015 at 12:40 AM Patricia Carvajal
<patriciacarvajal.mxli@xxxxxxxxx> wrote:
I'm trying to de novo assembly a set of mRNA sequences of a fasta (.fa)file,
there's no quality file on these sequences.--noqualities and
Per the assembly manaual the input file is a .fa file, the
-CL:pec=false parameters********************************************************************************
are stated in the manifest file as well as a default_qual=30.
[...]
Here's the error I'm getting...
* FASTA quality file expected to exist, but no quality filename given???*
Refer *
* to
*http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_manifest_readgroups*
* on how to load FASTA data without corresponding quality files.
There is a last security fence of MIRA (which is described in a somewhat
hidden
manner in the manual) trying to prevent you from doing something foolish or
going on when not all data is present: a FASTA file with the postfix
".fasta"
(or".fa") is expected to have a quality file present (named ".fasta.qual"
or
".fa.qual").
This check is not performed when reading FASTA files with a ".fna" postfix
or if
you force MIRA to treat a .fasta file as .fna file, the latter can be done
by
this:
data = fna::/cqd-dir/Cqd-mRNAs.fa
Regarding assembling without quality values, my usual warnings still apply:
simply don't do it. The longer version of this:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_never_without_quality_values
B.
------------------------------
Date: Tue, 6 Oct 2015 10:23:59 -0400 (EDT)
From: Bastien Chevreux <bach@xxxxxxxxxxxx>
Subject: [mira_talk] Re: Not finding HAsh Frequency tag colours in
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.
------------------------------
Date: Wed, 7 Oct 2015 09:43:57 +0530
Subject: [mira_talk] Re: Not finding HAsh Frequency tag colours in
From: Rameez Mj <rameez03online@xxxxxxxxx>
I am getting hash tags in contig editer but no colour code is available.
Sequence having all kinds of tags have same colour. Thanks Hoefler for your
suggestion I may need it in future cases.
On 6 October 2015 at 19:46, Chris Hoefler <hoeflerb@xxxxxxxxx> wrote:
You need to update the gap5 tag file with the Mira tags.{STADEN_PREFIX}/share/staden/etc/GTAGDB
cat {MIRA_PREFIX}/support/GTAGDB >>
you
You will likely need administrator access to do this. Restart gap5 and
should see all of the Mira tags.
On Mon, Oct 5, 2015 at 11:47 PM, Rameez Mj <rameez03online@xxxxxxxxx>
wrote:
I did an assembly with a manifest file which start like this
Project = 1247
Job = genome,denovo,accurate
parameters = -GE:not=4
parameters = -NW:cac=warn
I made a gap5 database from CAF output file. But there is no colour tag
available in gap5.All reads appear in a purple colour throughout the
sequence. What is happening should I invoke mira to tag wile assebly
separately?
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
------------------------------
Date: Wed, 7 Oct 2015 09:59:21 +0530
Subject: [mira_talk] Re: Not finding HAsh Frequency tag colours in
From: Rameez Mj <rameez03online@xxxxxxxxx>
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:
tagI made a gap5 database from CAF output file. But there is no colour
theavailable 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
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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------------------------------
Date: Wed, 7 Oct 2015 10:10:19 +0530
Subject: [mira_talk] Re: Not finding HAsh Frequency tag colours in
From: Rameez Mj <rameez03online@xxxxxxxxx>
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 startedor
using gap5 to find internal joints. How to decide if I join two contigs
not. I am attaching some screen shots please give me your suggestionabout
joining in those cases. In case 4, one side of overlap is clean andwhere
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
the mismatch starts. In some cases of mismatches one consensus have lowbase
base confidence(11) compared to other consensus(126) can I accept the
from second consensus and join the contigs?. Please share your muchvalued
opinion and suggestion in this.tag
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
theavailable 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
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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mailing list. For information on how to subscribe or unsubscribe, please
visit http://www.chevreux.org/mira_mailinglists.html
------------------------------
Date: Wed, 7 Oct 2015 10:12:05 +0530
Subject: [mira_talk] Re: Not finding HAsh Frequency tag colours in
From: Rameez Mj <rameez03online@xxxxxxxxx>
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 gettingthe
colour assisted hash tags.or
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
aboutnot. I am attaching some screen shots please give me your suggestion
wherejoining 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
basethe mismatch starts. In some cases of mismatches one consensus have low
base confidence(11) compared to other consensus(126) can I accept the
valuedfrom second consensus and join the contigs?. Please share your much
fileopinion 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
pleaseGTAGDB
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.
--
You have received this mail because you are subscribed to the mira_talk
mailing list. For information on how to subscribe or unsubscribe,
visit http://www.chevreux.org/mira_mailinglists.html
------------------------------
Date: Wed, 7 Oct 2015 10:12:29 +0530
Subject: [mira_talk] Re: Not finding HAsh Frequency tag colours in
From: Rameez Mj <rameez03online@xxxxxxxxx>
On 7 October 2015 at 10:12, Rameez Mj <rameez03online@xxxxxxxxx> wrote:
Please add this screenshot also in my previous query.Can I join thiscontigs or
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
aboutnot. I am attaching some screen shots please give me your suggestion
wherejoining 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
basethe mismatch starts. In some cases of mismatches one consensus have low
base confidence(11) compared to other consensus(126) can I accept the
valuedfrom second consensus and join the contigs?. Please share your much
wrote:opinion and suggestion in this.
On 6 October 2015 at 19:53, Bastien Chevreux <bach@xxxxxxxxxxxx>
mira_talk
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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------------------------------
End of mira_talk Digest V3 #112
*******************************
