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Forum: Bioinformatics 05-10-2013, 02:09 PM
Replies: 3
Views: 2,810
Posted By apadr007
I'm having the same problem. Any ideas,...

I'm having the same problem.

Any ideas, Loyal?
Forum: Bioinformatics 05-10-2013, 02:07 PM
Replies: 2
Views: 2,402
Posted By apadr007
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 -...
Forum: Bioinformatics 10-16-2012, 06:50 AM
Replies: 10
Views: 3,491
Posted By apadr007
When I say accession number I mean the name of...

When I say accession number I mean the name of the reference genes in your organism. This is found in the file you downloaded from whatever database you used.

No, you just get the accession...
Forum: Bioinformatics 10-16-2012, 05:07 AM
Replies: 10
Views: 3,491
Posted By apadr007
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...
Forum: Bioinformatics 07-18-2012, 12:32 PM
Replies: 16
Views: 12,810
Posted By apadr007
^ This would be helpful ^

^ This would be helpful ^
Forum: MGISEQ (FKA Complete Genomics) 05-21-2012, 01:24 PM
Replies: 3
Views: 2,992
Posted By apadr007
is there a program that has whole genome view of...

is there a program that has whole genome view of mapped read coverage? I know in IGV you can view only transcript abundance
Forum: Bioinformatics 04-25-2012, 11:42 AM
Replies: 3
Views: 2,876
Posted By apadr007
I am also having the same issue. I am using the...

I am also having the same issue. I am using the latest version of cummeRbund, however (1.2.0). The csSpecificity function is not working either. Any other ideas?
Forum: Genomic Resequencing 04-17-2012, 08:08 AM
Replies: 4
Views: 8,292
Posted By apadr007
Has anyone fold a solution to vcf files and...

Has anyone fold a solution to vcf files and circos?
Forum: Bioinformatics 04-09-2012, 12:57 PM
Replies: 16
Views: 12,810
Posted By apadr007
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...
Forum: Bioinformatics 04-06-2012, 01:08 PM
Replies: 16
Views: 12,810
Posted By apadr007
Since we're on the subject, what is the criteria...

Since we're on the subject, what is the criteria for something having significance in volcano plots?

I noticed that in some of my graphs my p-value may be less than 0.05 and not be significant...
Forum: Bioinformatics 03-15-2012, 12:28 PM
Replies: 4
Views: 2,706
Posted By apadr007
Did one of you guys find out what this does? I am...

Did one of you guys find out what this does? I am also curious.
Forum: Bioinformatics 03-06-2012, 06:50 AM
Replies: 6
Views: 2,638
Posted By apadr007
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...
Forum: Bioinformatics 12-13-2011, 12:40 PM
Replies: 2
Views: 1,544
Posted By apadr007
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...
Forum: Bioinformatics 12-13-2011, 07:12 AM
Replies: 3
Views: 4,176
Posted By apadr007
I have the same question. Why is cufflinks...

I have the same question. Why is cufflinks repeating genes?
Forum: Bioinformatics 12-13-2011, 06:59 AM
Replies: 2
Views: 1,544
Posted By apadr007
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 - - ...
Forum: Bioinformatics 11-23-2011, 09:43 AM
Replies: 2
Views: 2,276
Posted By apadr007
Can anyone shed some light -- 33 people have...

Can anyone shed some light -- 33 people have view, no one has posted
Forum: Bioinformatics 11-23-2011, 05:17 AM
Replies: 2
Views: 2,276
Posted By apadr007
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...
Forum: Bioinformatics 10-20-2011, 06:59 AM
Replies: 6
Views: 2,638
Posted By apadr007
...Anyone?

...Anyone?
Forum: Bioinformatics 10-18-2011, 10:24 AM
Replies: 6
Views: 2,638
Posted By apadr007
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...
Forum: Bioinformatics 10-17-2011, 05:41 AM
Replies: 10
Views: 3,491
Posted By apadr007
I had thought the generic overlap with a...

I had thought the generic overlap with a reference transcript only referred to single exon overlaps. Thanks, it seems I can use these class codes for my analysis.
Forum: Bioinformatics 10-16-2011, 09:35 AM
Replies: 10
Views: 3,491
Posted By apadr007
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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