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Search: Posts Made By: iloveneworleans
Forum: Bioinformatics 02-24-2010, 05:00 PM
Replies: 5
Views: 24,324
Posted By iloveneworleans
Thanks Simon very much! I thought Ensemble...

Thanks Simon very much!

I thought Ensemble is also an institute like European Biooinformatics Institute (EBI) and NCBI, actually Ensembl is a joint project between EMBL - EBI and the Wellcome...
Forum: Bioinformatics 02-24-2010, 11:05 AM
Replies: 5
Views: 24,324
Posted By iloveneworleans
Thanks Simon Andrews and Simon Anders! From...

Thanks Simon Andrews and Simon Anders!

From Ensemble and NCBI ftp server, we can get all complete assemblies. But I think EBI might have their own complete assemblies to download. As Simon Anders...
Forum: Bioinformatics 02-23-2010, 03:22 PM
Replies: 5
Views: 24,324
Posted By iloveneworleans
Where can I find the complete FASTA format sequence(human and mouse)?

On the EBI database website(http://www.ebi.ac.uk/astd/download.html), they only provide the FASTA format sequence of all exons or transcripts to download.
Anybody know where I can find the complete...
Forum: Bioinformatics 09-29-2009, 08:54 PM
Replies: 1
Views: 2,398
Posted By iloveneworleans
In gene annotation table/gff3, why is same gene name appeared in different chromosome

I found some genes with same gene name but in different chromosome, anyone knows the reason?
For example:
chr19 hg18_refFlat gene 763518 772952 . - . ID=PRG2;...
Forum: Bioinformatics 07-31-2009, 12:41 PM
Replies: 22
Views: 8,862
Posted By iloveneworleans
I just downloaded the latest Tophat-1.0.10, and...

I just downloaded the latest Tophat-1.0.10, and found there is an segment join failed error at the last.
And Tophat cannot generate the output files.
But the previous version did not have this...
Forum: Bioinformatics 07-31-2009, 12:24 PM
Replies: 22
Views: 8,862
Posted By iloveneworleans
I am using the Tophat-1.0.8 and Bowtie-0.9.9.3. ...

I am using the Tophat-1.0.8 and Bowtie-0.9.9.3.
From the accepted_hits.sam, I picked up some short-reads and and tried to search them on BLAT Search Genome (http://genome.ucsc.edu/cgi-bin/hgBlat),...
Forum: Bioinformatics 07-28-2009, 08:03 PM
Replies: 292
Views: 161,311
Posted By iloveneworleans
Thanks for nilshomer's help! Now the error...

Thanks for nilshomer's help!
Now the error message is disappeared.
But I only can see a black screen when I typed the command:
samtools tview aln.sorted.bam ref.fasta
I want to see how many...
Forum: Bioinformatics 07-27-2009, 10:12 PM
Replies: 292
Views: 161,311
Posted By iloveneworleans
I have a problem about converting sam format file...

I have a problem about converting sam format file into bam format file with samtools.
I downloaded the latest version:v0.1.5c
and my fasta file is about 3G; I met a "Bus error" when I run the below...
Forum: Bioinformatics 07-15-2009, 03:05 PM
Replies: 0
Views: 1,560
Posted By iloveneworleans
Tophat problem

I am trying to supply TopHat with a GFF3 file of gene annotation, the pipeline will report the relative expression of each in the sample.

But I don't know why the <GFF3_file>.expr file is empty...
Forum: RNA Sequencing 07-14-2009, 09:28 PM
Replies: 2
Views: 6,149
Posted By iloveneworleans
Where can I obtain GFF file for human?

I want to supply TopHat with a GFF3 file of gene annotation, the pipeline will report the relative expression of each in the sample.

Does anyone know where can I download the GFF file for human?...
Forum: Bioinformatics 07-14-2009, 09:07 PM
Replies: 14
Views: 14,023
Posted By iloveneworleans
1) To use TopHat, you will need the following...

1) To use TopHat, you will need the following Bowtie in your PATH:
* bowtie
* bowtie-inspect
* bowtie-build
In other words, you need to install Bowtie firstly and copy the above 3...
Forum: Bioinformatics 07-12-2009, 09:42 AM
Replies: 1
Views: 1,490
Posted By iloveneworleans
Question about GEF3 file

Hi all,

Does anybody know where I can download a GFF3 annotation file for human?

I am trying to use a GFF3 annotation file for human to generate the <GFF3_file>.expr with the Tophat. But I...
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