[mira_talk] Re: regd Mapping 454 titanium with Solexa paired reads
- From: Arun Rawat <rawat_arun@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 28 Mar 2011 18:38:36 -0700 (PDT)
Hi Bastein
________________________________
From: Bastien Chevreux <bach@xxxxxxxxxxxx>
To: mira_talk@xxxxxxxxxxxxx
Sent: Mon, March 28, 2011 12:07:03 PM
Subject: [mira_talk] Re: regd Mapping 454 titanium with Solexa paired reads
On Monday 28 March 2011 19:44:45 Arun Rawat wrote:
> I assembled bacterial genome from 454 Titanium that resulted in around 500
> contigs overall.
That is a fairly high number of contigs. Way to high to my likings. What's the
coverage of these?
1. Longer contigs (>=5000) are 125 in number (total contig count is 480):
Avg. total coverage (size >= 5000): 27.57.
> Now I am trying to use these sets of contigs to map paired reads to
> generate larger contigs. To test the results, I ran with default
> parameters: mira --project=mapSX_454 --job=mapping,genome,accurate,solexa
> -GE:not=16 -AS:nop=1 -SB:bft=caf >&log_assembly.txt
>
> The results came pretty good with higher N50, lesser number of contigs
> (~300) etc as mentioned in info_assembly.txt
Ahmmm ... something's not right here. If 500 contigs came in, 500 must come out
of a mapping assembly in the "All contigs" category: MIRA does not join contigs
in mapping. Can you please do a count on your input CAF for the number of
contigs with
grep -c Is_contig mapSX_454_backbone_in.caf
and tell what that gives you?
2. I think earlier file somehow got corrupted and I rerun it and found the
result consistent with the mapping file as you mentioned. I think I can try to
extract the contigs generated from solexa mapped against the 454 from ace file
generated. Do you think its right?
3. I also ran solexa paired read and 454 denovo (instead of mapping) and the
statistics are:
Assembly information:
=====================
Num. reads assembled: 6397880
Num. singlets: 0
Coverage assessment (calculated from contigs >= 5000):
=========================================================
Avg. total coverage: 102.61
Avg. coverage per sequencing technology
Sanger: 0.00
454: 27.85
PacBio: 0.00
Solexa: 74.42
Solid: 0.00
Large contigs (makes less sense for EST assemblies):
====================================================
With Contig size >= 500
AND (Total avg. Cov >= 34
OR Cov(san) >= 0
OR Cov(454) >= 9
OR Cov(pbs) >= 0
OR Cov(sxa) >= 24
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 157
Total consensus: 5348906
Largest contig: 542454
N50 contig size: 191948
N90 contig size: 32153
N95 contig size: 12196
Coverage assessment:
--------------------
Max coverage (total): 2134
Max coverage per sequencing technology
Sanger: 0
454: 1125
PacBio: 0
Solexa: 1606
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 85
Consensus bases with IUPAC: 135 (you might want to check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 71 (you might want to check
these)
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: 4926
Total consensus: 8216840
Largest contig: 542454
N50 contig size: 81331
N90 contig size: 561
N95 contig size: 346
Coverage assessment:
--------------------
Max coverage (total): 2134
Max coverage per sequencing technology
Sanger: 0
454: 1125
PacBio: 0
Solexa: 1606
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 78
Consensus bases with IUPAC: 2759 (you might want to check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 73 (you might want to check
these)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)
Any suggestions on these results!!
As mira does not allow to mix two directions from same technology, in the next
step I want to create longer contigs by mixing the contigs generated
(454+solexa paired end generated contigs as shown above) with the solexa mate
pair. Do you think the contigs generated (454+solexa paired end) can be
considered as sanger and the mate pair data added to create longer contigs. I
do
not want to scaffold now as we plan to use these long contigs as our reference
sequences for further studies.
Thanks!!
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