[mira_talk] Re: Assembling 454 and Solexa mate-pair data - rethinking ...
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 15 Sep 2009 11:23:26 +0200
I have tried yet another approach for this assembly. I assumed that the
Solexa data was contaminated, so I ran MIRA with the 454 contigs (used as
long Sanger reads) and the Solexa mate-pairs - but only the mate pairs that
could be mapped to the contigs (using Bowtie and allowing for 3 mismatches).
This reduced the amount of mate-pairs from 3M to 1M, and still reads should
be included that spans the gaps between the contigs.
So I fed the following to MIRA
mira -project=M1 -job=denovo,genome,normal,sanger,solexa
-GENERAL:number_of_threads=4 SOLEXA_SETTINGS -CO:msr=no
-GE:uti=no:tismin=2000:tismax=3000
M1_in.sanger.fasta
M1_in.solexa.fasta
And waited for a day and got:
Localtime: Tue Sep 15 10:51:42 2009
Assembly information:
=====================
Num. reads assembled: 1186418
Num. singlets: 20
Large contigs:
--------------
With Contig size >= 500
AND (Total avg. Cov >= 8
OR Cov(san) >= 0
OR Cov(454) >= 0
OR Cov(sxa) >= 8
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 915
Total consensus: 696521
Largest contig: 6010
N50 contig size: 739
N90 contig size: 538
N95 contig size: 523
Coverage assessment:
--------------------
Max coverage (total): 1625
Max coverage
Sanger: 0
454: 0
Solexa: 1625
Solid: 0
Avg. total coverage (size >= 5000): 23.75
Avg. coverage (contig size >= 5000)
Sanger: 0.00
454: 0.00
Solexa: 23.75
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 22
Consensus bases with IUPAC (IUPc): 645 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)
All contigs:
------------
Length assessment:
------------------
Number of contigs: 28134
Total consensus: 3312250
Largest contig: 6010
N50 contig size: 178
N90 contig size: 48
N95 contig size: 41
Coverage assessment:
--------------------
Max coverage (total): 1625
Max coverage
Sanger: 0
454: 0
Solexa: 1626
Solid: 0
Avg. total coverage (size >= 5000): 23.75
Avg. coverage (contig size >= 5000)
Sanger: 0.00
454: 0.00
Solexa: 23.75
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 19
Consensus bases with IUPAC (IUPc): 1542 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)
This strikes me as completely wrong. The long contigs are gone.
According to the log both Sanger and Solexa reads were loaded (I omitted the
quals on purpose expecting a simple run).
Martin
On Thu, Sep 10, 2009 at 5:09 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Donnerstag 10 September 2009 Martin A. Hansen wrote:
> > So, why are qualities so important? If you have enough sequence it should
> > level out?
>
> The "non-perfect-repeat" detection routines heavily rely on qualities to
> tag
> bases that aid to discern the different repeats. The base calling
> algorithms
> also take qualities into consideration when confronted to unsure
> situations.
>
> Plus a few other places where qualities do matter quite a lot :-)
>
> B.
>
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