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Search: Posts Made By: ECHo
Forum: Bioinformatics 08-29-2011, 07:28 AM
Replies: 3
Views: 6,160
Posted By ECHo
trinity error

Trinity is the new de novo transcriptome assembly software, and I'm interested in the the software.
According to the manual listed on the website, I tried to test it.
However, there are some errors...
Forum: De novo discovery 06-09-2011, 10:59 PM
Replies: 1
Views: 2,466
Posted By ECHo
Euler 2.0

I've tried to use EULER 2.0 to do the de novo assembly process.
However, there are error messages:
sh: line 1: 20961 Segmentation fault /home/echo/denovo/euler2_linux/trans_qual -i test.fasta...
Forum: RNA Sequencing 04-21-2011, 10:55 PM
Replies: 0
Views: 4,197
Posted By ECHo
SAM file for paired-end

I've aligned the Solexa data with tophat.
After doing the alignment, I got the bam file.
Since I want to find some fusion junction, which contains two different genes in one read, I have to search...
Forum: Bioinformatics 03-30-2011, 01:13 AM
Replies: 2
Views: 1,626
Posted By ECHo
Ooops! Actually, my .bashrc has a wrong $PATH...

Ooops!
Actually, my .bashrc has a wrong $PATH direction for the Python settings.
Thanks!
Forum: Bioinformatics 03-19-2011, 08:31 AM
Replies: 2
Views: 1,626
Posted By ECHo
Tophat error

I'm doing analysis with Solexa data, and I try to use Tophat.
However, I'm not sure why sometimes the system would throw out the error messages while sometimes it works correctly.

The error...
Forum: Bioinformatics 02-08-2011, 10:40 PM
Replies: 13
Views: 5,897
Posted By ECHo
Well, still one question: When I want to plot...

Well, still one question:
When I want to plot the MDS, I'd like to use the following command:
plotMDS.dge(d, xlim=c(-2,1));
d is a DGE object

However, the R system always shows the following:...
Forum: Bioinformatics 02-08-2011, 10:12 PM
Replies: 13
Views: 5,897
Posted By ECHo
haha I've found out the reason... Some data...

haha
I've found out the reason...
Some data include missing values.:)
Forum: Bioinformatics 02-08-2011, 09:24 PM
Replies: 13
Views: 5,897
Posted By ECHo
edgeR

I've read and used the DEGseq R-package.
And edgeR seems to be complement to DEGseq package.

But while manipulating with the edgeR manual, I insert some data into DGEList.
However, the counts...
Forum: Illumina/Solexa 02-25-2010, 07:21 PM
Replies: 0
Views: 2,030
Posted By ECHo
UCSC Genome Browser

I've uploaded the *.wig and *.bed files to UCSC Genome Browser Website.

Then, it shows the junction regions and read coverages.
As my realization, read coverage would be the matched part of...
Forum: Bioinformatics 02-19-2010, 11:57 PM
Replies: 4
Views: 4,894
Posted By ECHo
Well, I think the command would be as follows: ...

Well, I think the command would be as follows:
bowtie mm9 -r -n 1 -l 36 -a sequences-input -t 2> result

Maybe you should replace > with 2>
Forum: Bioinformatics 02-16-2010, 07:29 AM
Replies: 0
Views: 1,402
Posted By ECHo
Tophat and Bowtie

I know that Tophat would call bowtie to form fasta(*.fa) files as references.
And I use the command as follows:
./tophat -r 5 -p 12 chr22 ../TestData/s_1_1_seq.txt ../TestData/s_1_2_seq.txt

All...
Forum: Bioinformatics 02-15-2010, 02:59 AM
Replies: 0
Views: 3,925
Posted By ECHo
Cufflinks GTF file

The following is excepted from my gtf file, which is produced by Cufflinks:

chr21 Cufflinks transcript 14304464 14305055 1000 + . gene_id "CUFF.299";...
Forum: Bioinformatics 02-08-2010, 09:34 PM
Replies: 2
Views: 5,315
Posted By ECHo
Unhappy kind of weird... now it shows 1200%CPU ...

kind of weird...
now it shows 1200%CPU

Don't know why?
Forum: Bioinformatics 02-08-2010, 09:24 PM
Replies: 2
Views: 5,315
Posted By ECHo
Tophat Multi-Thread

Hi, I've used the following command:
./tophat -r 5 -p 12 ../bowtie-0.12.1/indexes/chr21 ../bowtie-0.12.1/TestData/s_1_1_sequence.txt ../bowtie-0.12.1/TestData/s_1_2_sequence.txt

-p 12 I think it...
Forum: Bioinformatics 02-07-2010, 08:51 PM
Replies: 12
Views: 4,074
Posted By ECHo
Well, that's why we must set PATH including...

Well, that's why we must set PATH including bowtie-build
bowtie-build can build *.ebwt through *.fa/*.fna

I think these steps can do the reverse...
So, it shows the same messages on fa/fna/ebwt...
Forum: Illumina/Solexa 02-02-2010, 01:00 AM
Replies: 0
Views: 1,360
Posted By ECHo
Problems about Bowtie

Our bench experimental data come from Solexa, which would offer us two BP ends.
Now, I'd like to use Bowtie to align the two end BP-sequencing with H. sapiens chromosomes.
Then, I use the following...
Forum: Introductions 02-02-2010, 12:46 AM
Replies: 0
Views: 1,200
Posted By ECHo
Hello

I'm new to Bowtie, which is one tool for sequencing.
It's good to find this place to discuss what might be encountered in analysis.
I use Bowtie on our LAB, Cent OS 5.2.

Though Bowtie is...
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