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bernardo_bello · 10-20-2012, 01:39 PM

Hello Bioinformatic community,
I recently entered in RNA-Seq world, I’m a second year PhD.
We have recently sequenced a bacterial transcriptome....

gaby · 10-09-2012, 07:17 AM

Hello everyone!
I wonder if anyone knows any way of, given a gff file and the corresponding genomic segment in fasta format, extract introns and...

wangxj · 09-17-2012, 11:43 PM

Hi all,

I have tryed the convert-tools form UCSC (link: http://hgdownload.cse.ucsc.edu/admin...gff3ToGenePred). But It seems,...

Hagen · 08-19-2012, 11:33 AM

Dear all,

I have some splice junctions (in GFF3) that I ultimately want to convert to bam. I was thinking to convert first to bed myself...

slowsmile · 08-05-2012, 10:38 AM

Dear all
We are recently working with E.coli plasmid and tried to summarize the gene counts from our RNA-Seq samples.
The short reads were...

Daniel Fernandez · 06-09-2012, 10:41 PM

Hi,

Can anybody tell me a program to find genes by homology that generate GFF3?

I tired AAT but only show me a table...

Daniel Fernandez · 06-07-2012, 12:16 PM

Hi,

We tried to work with Glimmer for prokaryotes annotation, but we need a GFF format to load in Artemis.
anybody can tell me ...

jgarbe · 09-07-2011, 11:21 AM

The NCBI Map Viewer has the latest pig genome build and shows the
locations of all the genes. I would like to download this gene
annotation...

ega2d · 07-28-2011, 06:40 AM

Hi all,

I have sucessfully completed an RNAseq pipeline with the old version of Cufflinks and I'm now trying to run the same data through...

naluru · 03-22-2011, 11:39 AM

Hello,

I downloaded some GFF files from ensembl website and only need a small subset of rows in these files. So, I opened them up in Excel...

jiexiong · 11-12-2010, 10:28 PM

Hi，everyone

I have now worked on my rna-seq data, and mapped the paired-end reads to the reference genome. For detected a background...

Darwin · 06-08-2010, 06:18 PM

Hi,

Does anyone know of an easy way to convert files in the SAM format to GFF (or GFF3)?

I do RNA-seq and have my output...

Bio.X2Y · 05-25-2010, 02:08 PM

Hi,

TopHat can accept user-specified junctions via a GFF3 file, so I'm trying to find a GFF3 file that represents the UCSC Gene model for...

Create GTF or GFF3 file from draft genome