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Forum: Bioinformatics 06-14-2014, 12:50 PM
Replies: 252
Views: 98,590
Posted By NGS group
waiting................

waiting................
Forum: Bioinformatics 06-13-2014, 02:23 PM
Replies: 252
Views: 98,590
Posted By NGS group
Is that possible to use already paired library for SSPACE

Hi all,

We normally use CLC bio for assembly, and CLC bio always pair the two Reads into one (i.e. R1.fastq + R2.fastq = pair.fastq).

However, in the SSPACE tutorial, the two Reads should be...
Forum: Bioinformatics 10-16-2013, 02:48 PM
Replies: 5
Views: 5,085
Posted By NGS group
Hi Peter, Thank you very much for your...

Hi Peter,

Thank you very much for your reply. That is what I want, and I will try it. I know this is not easy work. Before I tried GenoplotR, which is written by R. However the toturial is not...
Forum: Bioinformatics 10-16-2013, 03:40 AM
Replies: 5
Views: 5,085
Posted By NGS group
Question (Picture attached) how to plot/visulize gene synteny alignment

Hi,

Is there anyone can tell me some easy tools that can visulize/plot gene synteny alignment as the picture attached?

Thank you very much!

ZK
Forum: Bioinformatics 09-11-2013, 01:30 PM
Replies: 9
Views: 5,128
Posted By NGS group
Could you please show me the command line, since...

Could you please show me the command line, since I am quite new on linux system? Thank you very much!
Forum: Bioinformatics 09-11-2013, 12:52 PM
Replies: 9
Views: 5,128
Posted By NGS group
Because I need Phylip format file for building...

Because I need Phylip format file for building phylogenetic tree, which can not be produced by Mauve. I am not sure whether MUMer can generate the Phylip file. Do you know that?
Forum: Bioinformatics 09-11-2013, 12:06 PM
Replies: 9
Views: 5,128
Posted By NGS group
Unhappy The Muscle alignment

Hi,

I am trying to use Muscle to do alignment of 12 bacterial genomes in Linux 64bit OS, which was installed by Virtual Box in Win 7. However, I got the problem showed as follow:
...
Forum: Bioinformatics 08-09-2013, 04:39 AM
Replies: 4
Views: 1,309
Posted By NGS group
No one can give me any suggestion? It seems that...

No one can give me any suggestion? It seems that such kind of questions always have no answer in this forum.
Forum: Bioinformatics 08-08-2013, 05:20 AM
Replies: 4
Views: 1,309
Posted By NGS group
Question How to incorporate the reference into SNP tree

Hi everyone,

I am trying to build a SNP tree. The principle is to extract SNPs from each sample mapped to the reference to get a pseudo "SNP genome", and then multi-alignment will be performed...
Forum: Bioinformatics 08-06-2013, 08:13 AM
Replies: 6
Views: 3,005
Posted By NGS group
This is a nice web tool. Thank you very much,...

This is a nice web tool. Thank you very much, Jason.
Forum: Bioinformatics 08-05-2013, 01:11 PM
Replies: 6
Views: 3,005
Posted By NGS group
Hi Jason, Thank you for your reply. I am...

Hi Jason,

Thank you for your reply. I am working with 15-20 genomes, which have been assembled. I am using Mauve now, but I think it is not easy to filter the common sequences by manual in Mauve....
Forum: Bioinformatics 08-05-2013, 01:01 PM
Replies: 6
Views: 3,005
Posted By NGS group
Hi rhinoceros, Thank you for your reply. The...

Hi rhinoceros,

Thank you for your reply. The aim of my project is to distinguish outbreak strains, so I have to do the analysis by myself. The HAL pipeline is what I want exactly. However I am not...
Forum: Bioinformatics 08-05-2013, 07:20 AM
Replies: 6
Views: 3,005
Posted By NGS group
Question How to call the core genome of bacteria

Hi everyone,

I am trying to build a SNP tree from a set of bacterial genomes (the same species), and the first step is going to get the core genome. However, I did not find any detail workflow for...
Forum: Bioinformatics 07-30-2013, 11:57 PM
Replies: 12
Views: 7,789
Posted By NGS group
I found that this is not the reason of my...

I found that this is not the reason of my problem. Are there any other possibilities?
Forum: Bioinformatics 07-30-2013, 01:46 AM
Replies: 12
Views: 7,789
Posted By NGS group
The memory problem was due to the version of...

The memory problem was due to the version of Java. My computer is win 64bit, and both 32bit and 64 bit version of java have been installed. The program would use 32bit version automatically, which...
Forum: Bioinformatics 07-29-2013, 11:50 PM
Replies: 12
Views: 7,789
Posted By NGS group
Hi Sromero, Thanks for your reply. I already...

Hi Sromero,

Thanks for your reply. I already solved my problem. However, I get another problem is that I could not get all rings after running finished, even I tried with the Example data from...
Forum: Bioinformatics 07-26-2013, 04:10 AM
Replies: 12
Views: 7,789
Posted By NGS group
Angry Running errors showed by BRIG

Hi all,

I am trying to learn using BRIG for genome comparative study. I followed the manual step by step. However, after submitting my work, BRIG gave an error as follow:

"Rendering CGVIEW...
Forum: Bioinformatics 05-21-2013, 05:11 AM
Replies: 0
Views: 923
Posted By NGS group
The workflow for creating phylogenetic tree by SNPs

Dear all,

I will really appreciate if anyone would share their workflow for creating the phylogenetic tree by SNPs? Is there any commercial software that can do it?

Thank you very much!
...
Forum: Bioinformatics 05-21-2013, 05:09 AM
Replies: 10
Views: 12,388
Posted By NGS group
The workflow for creating phylogenetic tree by SNPs

Dear all,

I will really appreciate if anyone would share their workflow for creating the phylogenetic tree by SNPs? Is there any commercial software that can do it?

Thank you very much!
...
Forum: Bioinformatics 05-15-2013, 08:22 AM
Replies: 4
Views: 1,668
Posted By NGS group
OK, thank you very much for your helps. I am...

OK, thank you very much for your helps. I am going to have a try.
Forum: Bioinformatics 05-15-2013, 01:46 AM
Replies: 4
Views: 1,668
Posted By NGS group
Can I estimate the insert size based on the data...

Can I estimate the insert size based on the data of Bioanalyzer?
Forum: Bioinformatics 05-14-2013, 02:07 PM
Replies: 4
Views: 1,668
Posted By NGS group
Question How to set the distance of paired reads for de novo assembly?

Hi everyone,

I am using CLC bio to do the de novo assembly of bacterial genomes. I found that changing the setting of distance of paired reads during importing the raw data could significantly...
Forum: Bioinformatics 05-10-2013, 08:17 AM
Replies: 3
Views: 1,806
Posted By NGS group
Krobison, thanks for your reply. The coverage of...

Krobison, thanks for your reply. The coverage of the 2# run is around 140x. I used paired ends 2x250. The insertion size of the 2# run looks longer than that of the 1# run from Bioanalyzer data. The...
Forum: Bioinformatics 05-10-2013, 12:48 AM
Replies: 3
Views: 1,806
Posted By NGS group
Is there anyone can help me????

Is there anyone can help me????
Forum: Bioinformatics 05-09-2013, 12:32 PM
Replies: 3
Views: 1,806
Posted By NGS group
Smile Comparing the quality of de novo assembly from two runs' data

We are using Miseq to sequence microbial genomes (~5Mb). In the first run (1#), library containing 12 samples were sequenced, and 6 samples were sequenced in the other run (2#). Obviously, the data...
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