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Forum: Bioinformatics 12-30-2012, 04:37 AM
Replies: 0
Views: 740
Posted By xiongdianguang
Do some use the SplingViewer to generate Alternative splcing

I used a software splicingviewer to generate the alternative splcing ,But i found the results is significantly different with the results produced by BGI company. So i doubted the accuracy. Do you...
Forum: Bioinformatics 12-25-2012, 07:25 AM
Replies: 3
Views: 1,445
Posted By xiongdianguang
Excuse me,I want to ask you a question about, did...

Excuse me,I want to ask you a question about, did the link I give is a normal gff formation?
Forum: Bioinformatics 12-25-2012, 02:01 AM
Replies: 3
Views: 1,445
Posted By xiongdianguang
GTF convert to GFF

Hello everyone,I meet a problem in converting GTF format to a GFF format like the example in the http://122.228.158.106/SplicingViewer/data/RefGene_hg18.gff. The GTF format is the normal one. I try...
Forum: Bioinformatics 09-04-2012, 06:44 AM
Replies: 2
Views: 1,633
Posted By xiongdianguang
Hi hilmarberher, That i want to ask you,i...

Hi hilmarberher,
That i want to ask you,i am also confused about the gene's expression value produced by cufflinks and cuffdiff.there have different gene's expression value ,I don't know which...
Forum: Bioinformatics 09-03-2012, 08:13 AM
Replies: 2
Views: 1,633
Posted By xiongdianguang
Use cufflinks or cuffdiff to get gene expression value?

I used tophat cufflinks and cuffdiff to analysis my mRNA sequencing data, I am confused about the gene expression value. We have 7 samples in my expreiment, I can used cufflinks to produce every...
Forum: RNA Sequencing 09-03-2012, 08:05 AM
Replies: 7
Views: 1,930
Posted By xiongdianguang
by the way. you can try it after you run...

by the way. you can try it after you run cufflinks.Because the file produce by cufflinks is necessary when you run cuffdiff.
Forum: RNA Sequencing 09-03-2012, 08:02 AM
Replies: 7
Views: 1,930
Posted By xiongdianguang
I recommended you to read the paper<Transcript...

I recommended you to read the paper<Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation> .I want it can help you
Forum: RNA Sequencing 09-03-2012, 07:49 AM
Replies: 4
Views: 9,725
Posted By xiongdianguang
use cufflinks or cuffdiff to get the gene expression value?

I used tophat cufflinks and cuffdiff to analysis my mRNA sequencing data, I am confused about the gene expression value. We have 7 samples in my expreiment, I can used cufflinks to produce every...
Forum: Bioinformatics 04-30-2012, 06:28 PM
Replies: 0
Views: 1,171
Posted By xiongdianguang
Thumbs up about the tophat and cufflinks

Hello professors
I meet a problem during using the tophat and cufflinks to assembly our reads. We follow the instrunction of the protocol"Differential gene and transcript expression analysis of...
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