Forum: Bioinformatics
05-10-2013, 03:09 PM
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Replies: 3
Views: 2,942
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Forum: Bioinformatics
05-10-2013, 03:07 PM
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Replies: 2
Views: 2,496
same
I'm having the same problem
> head(fpkm(myGenes))
Error in head(fpkm(myGenes)) :
error in evaluating the argument 'x' in selecting a method for function 'head': Error in myFPKM$conf_hi -...
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Forum: Bioinformatics
10-16-2012, 07:50 AM
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Replies: 10
Views: 3,697
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Forum: Bioinformatics
10-16-2012, 06:07 AM
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Replies: 10
Views: 3,697
I want to revive this thread again as i am...
I want to revive this thread again as i am basically doing what apadr007 has plan to do sometime before. I did observed that class code "o" contained in some reference transcripts as well (same...
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Forum: Bioinformatics
07-18-2012, 01:32 PM
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Replies: 16
Views: 13,486
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Forum: MGISEQ (FKA Complete Genomics)
05-21-2012, 02:24 PM
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Replies: 3
Views: 3,216
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Forum: Bioinformatics
04-25-2012, 12:42 PM
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Replies: 3
Views: 3,010
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Forum: Genomic Resequencing
04-17-2012, 09:08 AM
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Replies: 4
Views: 8,661
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Forum: Bioinformatics
04-09-2012, 01:57 PM
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Replies: 16
Views: 13,486
Thank you, Loyal. Also, how can one generate a...
Thank you, Loyal. Also, how can one generate a table based on the data that csVolcano is plotting? The reason I ask is because after manually inspecting my cuff diff output I am not seeing some of...
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Forum: Bioinformatics
04-06-2012, 02:08 PM
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Replies: 16
Views: 13,486
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Forum: Bioinformatics
03-15-2012, 01:28 PM
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Replies: 4
Views: 2,824
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Forum: Bioinformatics
03-06-2012, 07:50 AM
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Replies: 6
Views: 2,932
Hi Ron, I also attempted to optimize certain...
Hi Ron, I also attempted to optimize certain parameters, however, if you go back to the cufflinks article you'll notice authors mention that they base their categorization of transcripts simply on...
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Forum: Bioinformatics
12-13-2011, 01:40 PM
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Replies: 2
Views: 1,643
This makes absolutely no sense to me. Cuffdiff...
This makes absolutely no sense to me. Cuffdiff generates an isoform file so it should simply report isoforms of a particular gene there, not in a file it calls "gene.exp.diff".
I guess it may do...
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Forum: Bioinformatics
12-13-2011, 08:12 AM
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Replies: 3
Views: 4,432
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Forum: Bioinformatics
12-13-2011, 07:59 AM
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Replies: 2
Views: 1,643
Cuffdiff multiple accession numbers
Hello,
I wanted to know why the Cuffdiff "gene.exp.diff" and "cds.diff" files were producing multiple accession numbers in the same row. For example:
XLOC_000122 - - ...
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Forum: Bioinformatics
11-23-2011, 10:43 AM
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Replies: 2
Views: 2,444
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Forum: Bioinformatics
11-23-2011, 06:17 AM
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Replies: 2
Views: 2,444
Downstream Cuffdiff analysis
Hi guys,
I am working on the downstream analysis of my rna seq data using Cufflinks, Cuffcompare, and Cuffdiff. I basically want to know three simple questions that I am having a lot of difficulty...
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Forum: Bioinformatics
10-20-2011, 07:59 AM
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Replies: 6
Views: 2,932
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Forum: Bioinformatics
10-18-2011, 11:24 AM
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Replies: 6
Views: 2,932
minimum depth of coverage for transfrag extension
Hello,
I am wondering why cufflinks is creating transcript model extensions based on low depth of coverage (see the red highlighted box in the attached image). So the reference annotation is in...
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Forum: Bioinformatics
10-17-2011, 06:41 AM
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Replies: 10
Views: 3,697
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Forum: Bioinformatics
10-16-2011, 10:35 AM
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Replies: 10
Views: 3,697
Cufflinks and Cuffcompare extended CDS?
Hello,
I have just finished running cufflinks on my dataset and I would like to know how to calculate how much the coding regions of the cufflinks transcript models extended past the known...
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