Forum: Bioinformatics
02-02-2015, 09:16 AM
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Replies: 8
Views: 8,822
Hi Jen,
I'm not sure if there is a way to...
Hi Jen,
I'm not sure if there is a way to use the log2foldchange for coloring of the data points. You'd definitely have to open it up to see how they define the variables. You may be better off...
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Forum: General
01-28-2014, 08:30 AM
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Replies: 31
Views: 15,788
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Forum: General
01-28-2014, 08:14 AM
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Replies: 31
Views: 15,788
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Forum: Bioinformatics
01-09-2014, 12:12 PM
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Replies: 4
Views: 1,621
Using upwards of 600 million reads, I have...
Using upwards of 600 million reads, I have aligned the reads to the reference genome using the Tuxedo suite of programs and using a RABT assembly. This gives me around 10,000 completely unknown...
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Forum: General
12-17-2013, 08:04 AM
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Replies: 31
Views: 15,788
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Forum: Bioinformatics
12-05-2013, 07:23 AM
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Replies: 8
Views: 8,822
Hi Jason,
I just found the reasoning for why...
Hi Jason,
I just found the reasoning for why cuffdiff doesn't report any p-value less than 0.0001, and it can be found at this website: http://sihua.us/Cufflinks.htm
In short it says: The range...
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Forum: Bioinformatics
12-04-2013, 02:08 PM
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Replies: 8
Views: 8,822
Hi Jason,
Did you ever find an answer to...
Hi Jason,
Did you ever find an answer to this question? I am having a similar problem with my volcano plots with a "ceiling" of the same as yours and am wondering how to correct for it?
-Adam
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Forum: RNA Sequencing
11-20-2013, 01:09 PM
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Replies: 5
Views: 2,008
I have found the culprit of the problem. It...
I have found the culprit of the problem. It seems that the sequencing institute aligned the reads to the genome, which makes us think that they received reads and then aligned them genome. In...
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Forum: RNA Sequencing
11-20-2013, 07:33 AM
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Replies: 5
Views: 2,008
dpryan, I just contacted the institute that...
dpryan, I just contacted the institute that aligned the files and the didn't use any splice junction aligned like tophat or PASTA, which I foolishly assumed. As they won't send me the read files as...
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Forum: RNA Sequencing
11-20-2013, 07:19 AM
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Replies: 5
Views: 2,008
RNA-seq not showing splice junctions
I have two RNA-seq data sets. When one is run through Cufflinks I see isoforms but when I run the other I see no isoforms, only single exons/transcripts, none with multiple exons. Further...
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Forum: Bioinformatics
11-19-2013, 02:52 PM
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Replies: 7
Views: 3,539
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Forum: Bioinformatics
11-12-2013, 11:37 AM
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Replies: 4
Views: 1,621
Cufflinks novel gene discovery
I have two questions regarding novel gene discovery using Cufflinks:
1.) Does anyone have a good answer for what the appropriate FPKM cutoff value should be during gene discovery using Cufflinks. ...
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Forum: RNA Sequencing
11-10-2013, 12:34 PM
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Replies: 1
Views: 2,010
Cufflinks Killed Before Complete
I am attempting a RABT assembly of a genome which contains contigs 2L,2R,3L,3R,X, Y_unplaced and UNKN. Cufflinks inspects bundles for each of the 7 contigs provided from the GTF file but when it...
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