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Forum: Bioinformatics 09-24-2013, 02:33 AM
Replies: 0
Views: 1,304
Posted By jjjscuedu
smRNA sequence analysis without reference genome

Dear all,

I have some Illumina smRNA sequence results, but without reference genome, only some transcriptome data.

Hence, I think I should align these reads into the mature sequence from...
Forum: Bioinformatics 08-20-2013, 04:48 AM
Replies: 0
Views: 1,336
Posted By jjjscuedu
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....
Forum: Bioinformatics 08-13-2013, 07:22 PM
Replies: 0
Views: 1,278
Posted By jjjscuedu
difference between pair end and single end reads assembly

Dear all,

I have a little question about the difference pair end and single end assembly.

For most of the de bruijn based assembly algorithm, they try to construct kmer based graph. Hence, for...
Forum: Bioinformatics 07-01-2013, 07:34 PM
Replies: 0
Views: 1,356
Posted By jjjscuedu
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...
Forum: Literature Watch 06-12-2013, 09:11 AM
Replies: 29
Views: 22,593
Posted By jjjscuedu
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...
Forum: Bioinformatics 05-06-2013, 02:03 PM
Replies: 252
Views: 106,407
Posted By jjjscuedu
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...
Forum: Bioinformatics 04-12-2013, 10:47 AM
Replies: 2
Views: 1,012
Posted By jjjscuedu
My genome is about 1800Mb. The machine of my...

My genome is about 1800Mb.

The machine of my server is about Red hat Enterprise Linux 6.3 64bit, 10CPU.
Forum: Bioinformatics 04-11-2013, 08:02 PM
Replies: 2
Views: 1,012
Posted By jjjscuedu
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...
Forum: Bioinformatics 04-03-2013, 11:23 AM
Replies: 2
Views: 1,452
Posted By jjjscuedu
Does anyone have a good solution for this...

Does anyone have a good solution for this problem?

I am also confuse why cuffdiff does not utilize multiple threads after mapping. Too slow to large scale date set.
Forum: Bioinformatics 11-28-2012, 04:07 PM
Replies: 2
Views: 4,692
Posted By jjjscuedu
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...
Forum: Bioinformatics 10-12-2012, 05:41 PM
Replies: 1
Views: 984
Posted By jjjscuedu
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
Forum: Bioinformatics 06-14-2012, 05:48 PM
Replies: 0
Views: 834
Posted By jjjscuedu
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]$...
Forum: Bioinformatics 06-14-2012, 05:05 PM
Replies: 4
Views: 3,949
Posted By jjjscuedu
I have put the name of file in the txt file like...

I have put the name of file in the txt file like this:

/diag/home/jjin/oil_palm/raw/DNA1.fastq
/diag/home/jjin/oil_palm/raw/DNA2.fastq

However, it still display error for the second file:
...
Forum: De novo discovery 06-14-2012, 08:23 AM
Replies: 7
Views: 2,977
Posted By jjjscuedu
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...
Forum: Bioinformatics 06-06-2012, 12:33 PM
Replies: 3
Views: 2,727
Posted By jjjscuedu
if in.fa contains multiple sequence file, there...

if in.fa contains multiple sequence file, there will be an error message like this:

faToNib only works on fa files containing a single sequence.
Forum: Bioinformatics 06-06-2012, 11:48 AM
Replies: 2
Views: 1,578
Posted By jjjscuedu
Did you find the solution for this problem?

Did you find the solution for this problem?
Forum: Bioinformatics 06-06-2012, 11:47 AM
Replies: 3
Views: 2,727
Posted By jjjscuedu
Does Blat can take multiple reference sequence in one command line

I have successfully used blat executable on my system, but the problem is i am able to take only one reference sequence as reference database against query sequences.

Now i want to take multiple...
Forum: Bioinformatics 06-01-2012, 02:01 PM
Replies: 2
Views: 2,067
Posted By jjjscuedu
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...
Forum: Bioinformatics 06-01-2012, 01:58 PM
Replies: 1
Views: 1,322
Posted By jjjscuedu
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:
...
Forum: De novo discovery 05-23-2012, 07:12 PM
Replies: 9
Views: 3,420
Posted By jjjscuedu
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...
Forum: De novo discovery 05-19-2012, 12:58 PM
Replies: 3
Views: 4,156
Posted By jjjscuedu
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...
Forum: Bioinformatics 05-01-2012, 12:27 PM
Replies: 1
Views: 3,577
Posted By jjjscuedu
how to align the contigs to the reference genome

Hi all,

I am trying to do the de-novo assembly for my RNAseq dataset. First, I want to compare the accuracy of different assembly tools.

Hence, I select one RNAseq data which already a...
Forum: De novo discovery 04-26-2012, 07:40 AM
Replies: 0
Views: 1,182
Posted By jjjscuedu
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 ...
Forum: De novo discovery 04-25-2012, 08:56 AM
Replies: 2
Views: 7,934
Posted By jjjscuedu
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...
Forum: Bioinformatics 04-19-2012, 05:18 PM
Replies: 0
Views: 1,525
Posted By jjjscuedu
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...
Showing results 1 to 25 of 35

 


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