I am not sure what this does.
On my end, I have a tool that detects duplicated sequences in an assembly.
Mitchell Stanton-Cook a écrit :
Hi Seb,
I've been using cd-hit-est to investigate.
Attached is a simple python script and shell script that you can craft
to suit your environment. It may be useful for debugging.
Also attached is a sample output (which I've truncated below)
1 >Cluster 0
2 0 271623nt, >19_contig-1000000... at +/100.00%
3 1 63731nt, >19_contig-3... at +/100.00%
4 2 346149nt, >21_contig-8000003... *
5 3 243006nt, >23_contig-1000002... at +/100.00%
6 4 330249nt, >25_contig-9000002... at +/100.00%
7 5 63731nt, >27_contig-1000002... at +/100.00%
8 6 271674nt, >27_contig-7000002... at -/99.99%
9 7 63749nt, >29_contig-4000000... at +/100.00%
10 8 242978nt, >29_contig-11000002... at +/100.00%
We'd hope not to have multiple entries for the kmer in a cluster.
Hope this is useful,
Regards
Mitch
On Fri, May 25, 2012 at 11:35 AM, Mitchell Stanton-Cook
<m.stantonc...@gmail.com <mailto:m.stantonc...@gmail.com>> wrote:
Hi Seb,
Thank you. We're still doing some more work this end. We really
really really like Ray! We are more than happy to work through
these problems.
We hope to be pushing <information redacted> through Ray in a few
months. We just want to be sure that we are getting useful results.
If there is anything else we can do to help/bugfix please do not
hesitate to let us know.
Regards
Mitch
On Fri, May 25, 2012 at 11:23 AM, Sébastien Boisvert
<sebastien.boisver...@ulaval.ca
<mailto:sebastien.boisver...@ulaval.ca>> wrote:
Just to let you know that I may have found the problem.
See https://github.com/sebhtml/ray/issues/55
Sébastien
________________________________________
De : Mitchell Stanton-Cook [m.stantonc...@gmail.com
<mailto:m.stantonc...@gmail.com>]
Date d'envoi : 17 mai 2012 22:32
À : Sébastien Boisvert
Objet : Re: Duplicate sequence in contigs
Hi Seb,
Thanks for the reply.
A bit more background:
-------------------------------
This is 100 bp Illumina PE data (insert of ~300 bp s.d of
about ~10%).
~ 1000X coverage. Ray (1.7) did not like this high coverage
(you have previously commented on the user-list about this).
We sampled this down to ~100X coverage.
We also cleaned the reads (you have pointed this is not
necessary, but having a consistent cleaned set makes
downstream analysis i.e. snp calling much easier). All input
bases have a Q score >= 30. Reads > 70bp after trimming were
filtered. After this the mean reads size is ~97 bp. We only
consider read pairs (if 1 one of the sequences in the pairs
fails a cleaning criterion, both do) and hence no single end
reads go into Ray.
Ray was executed like this (we used Ray's internal
estimations/calculations to determine the best parameters):
mpiexec -n $PROC Ray -i XXXX.fastq -k $K -o $OUT
We looked at kmers from 15-35 in increments of 2.
The genome is ~1.8 Mb. From the assemblies it appears there
are not a lot repetitive elements in the genome. I have
attached a csv of the results (XXXX_ALL.csv) ( abbreviations:
c= contigs, s= scaffold, N = scaffolding character).
Results for kmer 21 and kmer 23 are interesting.
kmer 21) As previously mentioned we have a 63 Kb duplication.
For 63 Kb the start of the two contigs are almost identical (3
mismatches and 1 gap):
Score = 1.165e+05 bits (63086), Expect = 0.0
Identities = 63093/63096
<tel:63093%2F63096><tel:63093%2F63096> (99%), Gaps = 1/63096 (0%)
Strand=Plus/Plus
I have attached the alignment (XXXX_b2s.aln)
There is also a smaller 5 Kb duplication detected:
Score = 9583 bits (5189), Expect = 0.0
Identities = 5192/5193 (99%), Gaps = 1/5193 (0%)
Strand=Plus/Minus
kmer 23) (Notice there is about 63 Kb difference between the
"c 100 bp total len" in the .csv file of kmer 21 and kmer 23).
From the blast2seq there is no such 63 Kb duplication found.
Now, once again focusing on the "c 100 bp total len" in the
.csv file. I propose kmer 21 duplicate, kmer 23 no-duplicate,
kmer 25 non-duplicate, kmer 27 duplicate (I verified this
true), kmer 29 non-duplicate. Strangely kmer 31 is missing
about 200 Kb in comparison to the other assemblies.
What we are wondering is:
1) Why is there large, almost identical duplicates present in
the assemblies?
2) Why do we see it in some kmers and not others? (I could
understand if lower kmer = duplicates, higher kmers =
non-duplicates if these duplicates are propagated by a
sequencing error)
3) Is this a bug or an inherit issue with graph based assembly?
4) If possible, how can we fix this?
5) How can I help you with this?
I hope I have provided you with enough information. If not
please let me know.
p.s. I have know problem with this going to the list as long
as the attachments are not included.
Regards
Mitch
On Fri, May 18, 2012 at 12:25 AM, Sébastien Boisvert
<sebastien.boisver...@ulaval.ca
<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca
<mailto:sebastien.boisver...@ulaval.ca>>> wrote:
Hi,
Is the 63 kB perfectly duplicated in your assembly ?
Le 2012-05-17 01:26, Mitchell Stanton-Cook a écrit :
Hi Seb,
Hope all is well.
I was wondering if you have ever seen duplicate sequence in
contigs.
We have ~63 kB duplicate at the start of two different
contigs. Beyond this it's unique.
This is Ray 1.7.
I'm re-running with Ray2.0rc5.
I came across these posts (ABySS specific):
http://groups.google.com/group/abyss-users/browse_thread/thread/264e894b4ec0c96d/30dab75afa686878
http://groups.google.com/group/abyss-users/browse_thread/thread/7a03ee033b11afc4
http://groups.google.com/group/abyss-users/browse_thread/thread/f0f3a650bd12cf1e
Any ideas?
Regards
Mitch
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