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Search: Posts Made By: robertorun
Forum: RNA Sequencing 02-09-2016, 03:50 PM
Replies: 0
Views: 1,296
Posted By robertorun
DESeq2 with different replicates

There are 104 samples, 38 samples are treated, 66 samples are control. The following script was used to do DGE analysis. But there is no any different expression genes, even though using the...
Forum: De novo discovery 07-08-2012, 07:04 PM
Replies: 1
Views: 1,797
Posted By robertorun
I also met the same errors. I only downloaded...

I also met the same errors.
I only downloaded the lastest velvet and oases , then recompile them , now ,they are work smoothly!
Forum: Bioinformatics 09-09-2010, 04:30 PM
Replies: 6
Views: 5,358
Posted By robertorun
I think, the key is the caculation of level!

I think, the key is the caculation of level!
Forum: Bioinformatics 07-21-2010, 04:51 AM
Replies: 4
Views: 2,143
Posted By robertorun
i also find the bug, but i email to 454 Roche...

i also find the bug, but i email to 454 Roche company and don't get the answer.

Through comparision, the lenght=72 maybe the length longer than another contig from the same isotig. For example,...
Forum: Bioinformatics 06-10-2010, 04:15 AM
Replies: 3
Views: 4,478
Posted By robertorun
It's a good tool. I have use it!

It's a good tool. I have use it!
Forum: Bioinformatics 06-06-2010, 11:31 PM
Replies: 23
Views: 18,102
Posted By robertorun
I use Fedora,but the Fedora is updated so fast...

I use Fedora,but the Fedora is updated so fast and only surpport server about 1 half year, so wang to use RedHat AS or CentOS.
Forum: Bioinformatics 06-02-2010, 07:17 PM
Replies: 3
Views: 2,090
Posted By robertorun
tell me the different between two version cap?

Recently , i have used two version cap3, the before version is buided at 04/15/05, the latest VersionDate is 10/15/07.

when i used the two version software to assemble the following datasets with...
Forum: Bioinformatics 06-02-2010, 02:24 AM
Replies: 7
Views: 2,644
Posted By robertorun
Fedora7-64bit, it's a little out of time!

Fedora7-64bit, it's a little out of time!
Forum: Bioinformatics 05-26-2010, 07:09 PM
Replies: 24
Views: 4,331
Posted By robertorun
Thanks! I have read your paper and also will try...

Thanks! I have read your paper and also will try to run this scripts!
Forum: Bioinformatics 05-25-2010, 05:39 AM
Replies: 24
Views: 4,331
Posted By robertorun
is the psubprocess all the package of...

is the psubprocess all the package of NGS_backbone???:p
Forum: Bioinformatics 05-25-2010, 05:29 AM
Replies: 24
Views: 4,331
Posted By robertorun
OK,thanks! I will try

OK,thanks! I will try
Forum: Bioinformatics 05-25-2010, 05:19 AM
Replies: 24
Views: 4,331
Posted By robertorun
the 0.1 release

the 0.1 release
Forum: Bioinformatics 05-25-2010, 04:56 AM
Replies: 24
Views: 4,331
Posted By robertorun
excute the command: python ./backbone_analysis.py...

excute the command: python ./backbone_analysis.py -s ./temp001/ -a temp001

the error is following:

<type 'exceptions.KeyError'>
Python 2.6.5: /usr/local/bin/python
Tue May 25 20:11:43 2010
...
Forum: Bioinformatics 05-25-2010, 03:06 AM
Replies: 24
Views: 4,331
Posted By robertorun
I have installed the biopython and pyrex after...

I have installed the biopython and pyrex after downloading from web, then excute ngs_backbone, the following is thas,but there is backbone.conf file under the temp001 fold.

python...
Forum: Bioinformatics 05-25-2010, 01:25 AM
Replies: 24
Views: 4,331
Posted By robertorun
The version of Python is 2.6.5. It's downloaded...

The version of Python is 2.6.5. It's downloaded from http://www.python.org/ and installed. The biopython is installed bu the following command:

yum install python-biopython

[ydj@cotton-dell...
Forum: Bioinformatics 05-25-2010, 12:42 AM
Replies: 24
Views: 4,331
Posted By robertorun
My OS is fedora 7, the biopython and pyrex is...

My OS is fedora 7, the biopython and pyrex is already intalled.

Jose ,would you like to send the modified psubprocess package to me? Because of there much lilltle files. My email is...
Forum: Bioinformatics 05-24-2010, 11:45 PM
Replies: 24
Views: 4,331
Posted By robertorun
python ngs_backbone_analysis.py -a temp001 ...

python ngs_backbone_analysis.py -a temp001
python: can't open file 'ngs_backbone_analysis.py': [Errno 2] No such file or directory
[root@cotton-dell scripts-2.6]# python backbone_analysis.py -a...
Forum: Bioinformatics 05-24-2010, 11:19 PM
Replies: 24
Views: 4,331
Posted By robertorun
But when i execute the 'python...

But when i execute the 'python ./backbone_create_project.py -p temp001', it's successed!
Forum: Bioinformatics 05-24-2010, 11:13 PM
Replies: 24
Views: 4,331
Posted By robertorun
I have installed the configobj successfully, but...

I have installed the configobj successfully, but when i try to install pysam-0.2 and psubprocess-0.1.0, the same error is following

pysam-0.2]# python ./setup.py install
Traceback (most recent...
Forum: Bioinformatics 05-24-2010, 07:55 PM
Replies: 24
Views: 4,331
Posted By robertorun
I have install MIRA 3 succesully and run it. But...

I have install MIRA 3 succesully and run it. But ,when I rum NGS_backbone , it's error.

python ./backbone_create_project.py -p temp001

Traceback (most recent call last):
File...
Forum: Bioinformatics 05-21-2010, 03:59 AM
Replies: 24
Views: 4,331
Posted By robertorun
Thanks for Jose Blanca's answer! I tried to...

Thanks for Jose Blanca's answer!

I tried to insall MIRA ,but it's also failure. Becuase the OS is fedora7, and the latest version of python and boostlib under this OS is 2.5 and 1.3 respectively....
Forum: Bioinformatics 05-20-2010, 07:15 PM
Replies: 24
Views: 4,331
Posted By robertorun
Wink How to assembel more than two million ESTs sequnces?

There is a project which need a referrence sequences, so i collect all the ESTs sequences and four 454 datasets from NCBI and modify to fasta format.

I tried to cluster and asemble with tgicl, but...
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