Forum: Bioinformatics
09-24-2013, 02:33 AM
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Replies: 0
Views: 1,337
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Forum: Bioinformatics
08-20-2013, 04:48 AM
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Replies: 0
Views: 1,349
visualize linkage map and assembly scaffold
Dear all,
I want to visualize the relationship between my linkage map and my assembly scaffold.
Does anyone know some tools to do this work?
The figure is similar with the attachment figure....
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Forum: Bioinformatics
08-13-2013, 07:22 PM
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Replies: 0
Views: 1,304
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Forum: Bioinformatics
07-01-2013, 07:34 PM
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Replies: 0
Views: 1,367
smRNA sequence analysis
Dear all,
I have some smRNA sequence data from Illumina.
However, I don't find a suitable tool to analysis it yet.
Can someone give me some suggestions about how to deal with it?
For my...
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Forum: Literature Watch
06-12-2013, 09:11 AM
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Replies: 29
Views: 22,727
ray moi running problem
Dear all,
I am trying to run Ray on a test data.
However, when I try to run it according to the mannual, there is an error like this:
[jingjing@tll-bioinfo02 Ray-v2.2.0]$ mpiexec -n 1...
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Forum: Bioinformatics
05-06-2013, 02:03 PM
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Replies: 252
Views: 106,934
SSPACE error
Dear all,
I have a pair end 454 library, which I extract pair end sequence by myself into two files like this:
left
>H68R2DI01DH3A5/1...
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Forum: Bioinformatics
04-12-2013, 10:47 AM
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Replies: 2
Views: 1,028
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Forum: Bioinformatics
04-11-2013, 08:02 PM
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Replies: 2
Views: 1,028
how to speed up minimus2
Dear all,
I am now trying to use minimus2 to merge assembly results from two different assembly tools.
However, after running two weeks, minimus2 is still on the nucmer step.
Can anyone give...
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Forum: Bioinformatics
04-03-2013, 11:23 AM
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Replies: 2
Views: 1,478
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Forum: Bioinformatics
11-28-2012, 04:07 PM
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Replies: 2
Views: 4,729
rnammer running error
Does anyone use the RNAmmer software to scan genome to find rRNA?
I have already edited the path of rnammer file including the path to hmmsearch.
However, when I run it like this on sample...
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Forum: Bioinformatics
10-12-2012, 05:41 PM
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Replies: 1
Views: 1,002
bowtei for multiple pair end library
Dear all,
I want to use bowtie to generate the sam file for my pair end file.
However, I have several pair end file like this:
lib1_1.fq lib1_2.fq
lib2_1.fq lib2_2.fq
lib3_1.fq lib3_2.fq
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Forum: Bioinformatics
06-14-2012, 05:48 PM
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Replies: 0
Views: 851
samtoafg
Dear all,
After running SOAP assembly, I am trying to scaffold them using bambus2.
However, when I convert the contig file into afg file, there is an
error like this:
[jjin@fnode1 bambus2]$...
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Forum: Bioinformatics
06-14-2012, 05:05 PM
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Replies: 4
Views: 3,976
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Forum: De novo discovery
06-14-2012, 08:23 AM
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Replies: 7
Views: 2,995
I also have this problem.
From the...
I also have this problem.
From the SOAPdenovo log, it seems about 90% reads align to the contig.
However, when I use the bowtie trying to align the raw reads to the contig file, it is also just...
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Forum: Bioinformatics
06-06-2012, 12:33 PM
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Replies: 3
Views: 2,750
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Forum: Bioinformatics
06-06-2012, 11:48 AM
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Replies: 2
Views: 1,602
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Forum: Bioinformatics
06-06-2012, 11:47 AM
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Replies: 3
Views: 2,750
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Forum: Bioinformatics
06-01-2012, 02:01 PM
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Replies: 2
Views: 2,102
abyss-pe error
For the ABySS, I can run it successfully local.
However, when I submit a job to sever like this, there is always an error message like this:
which: no mpirun in...
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Forum: Bioinformatics
06-01-2012, 01:58 PM
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Replies: 1
Views: 1,334
velvet running error
Dear all,
I think I have installed the velvet successfully, because it is OK several days ago.
However, when I run the velvet today, I find there always an error like this:
...
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Forum: De novo discovery
05-23-2012, 07:12 PM
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Replies: 9
Views: 3,445
cloud computing sever for DNA sequence assembly
Dear all,
Do you know some famous cloud computing sever for DNA sequence assembly?
Because my sequence dataset is too large: 450 million for one end, 900 million for pair end.
I have checked...
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Forum: De novo discovery
05-19-2012, 12:58 PM
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Replies: 3
Views: 4,177
De novo assembly from DNA sequence and RNA seq
Hi all,
I want to ask a question about the difference between DNA sequence and RNA sequence assembly.
Do they have any difference?
For DNA sequence, which is suitable?
Because I see the...
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Forum: Bioinformatics
05-01-2012, 12:27 PM
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Replies: 1
Views: 3,670
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Forum: De novo discovery
04-26-2012, 07:40 AM
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Replies: 0
Views: 1,203
velvet parameter setting
Dear all,
I am now trying to use the velvet to analysis my RNAseq dataset.
I haven't set the advance parameter yet.
./velveth /diag/home/jjin/rice/leaf/velvet/k35/ 35 -fastq -shortPaired ...
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Forum: De novo discovery
04-25-2012, 08:56 AM
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Replies: 2
Views: 7,956
trinity error
I try to run the trinity for my RNA-seq dataset, but get the following errors:
CMD finished (0 seconds)
CMD: /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm --kmers...
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Forum: Bioinformatics
04-19-2012, 05:18 PM
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Replies: 0
Views: 1,537
Quake install problem
hi all,
When I install the Quake, I install the Jellyfish under /usr/local/bin folder.
Then I have changed the jellyfish_dir to /usr/local/bin;
However, when I try to run the command like...
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