Forum: Bioinformatics
06-15-2012, 11:22 AM
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Replies: 46
Views: 20,051
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Forum: Bioinformatics
06-15-2012, 11:21 AM
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Replies: 46
Views: 20,051
Hi Mat,
That sounds fair to me - Cuffdiff 2...
Hi Mat,
That sounds fair to me - Cuffdiff 2 is far more conservative at the gene level than was 1.3 (as detailed on the site), and with a single replicate per sample, even more so. This isn't too...
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Forum: RNA Sequencing
06-15-2012, 10:37 AM
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Replies: 67
Views: 74,323
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Forum: Bioinformatics
06-12-2012, 07:30 AM
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Replies: 46
Views: 20,051
Hmm, we see that sometimes when one or more of...
Hmm, we see that sometimes when one or more of the libraries have extremely low sequencing yield, for example. Can you show me a csDendro plot with replicates=T? It's important to verify that the...
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Forum: Bioinformatics
06-11-2012, 05:17 AM
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Replies: 46
Views: 20,051
We are testing a pre-release that fixes the...
We are testing a pre-release that fixes the issues reported so far, at least in our hands. Can you try:
http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.0.1.Linux_x86_64.tar.gz
(No mac...
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Forum: Bioinformatics
06-02-2012, 04:21 PM
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Replies: 46
Views: 20,051
I should also point out that this doesn't...
I should also point out that this doesn't necessarily mean there's a problem - Cuffdiff 2 tends to report fewer DE genes than other tools such as DESeq or edgeR, because these tools don't incorporate...
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Forum: Bioinformatics
06-02-2012, 04:18 PM
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Replies: 46
Views: 20,051
Another user has reported this to us, but we...
Another user has reported this to us, but we haven't been able to reproduce it ourselves. Can you send us a small test set of data that we can use to debug this? If you're willing to share the test...
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Forum: Bioinformatics
06-02-2012, 04:15 PM
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Replies: 46
Views: 20,051
I was asking if you still see few significant...
I was asking if you still see few significant genes and many NOTESTs when you use the reference GTF with Cuffdiff instead of the one you assembled.
It sounds like there are two different things...
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Forum: Bioinformatics
06-01-2012, 04:52 AM
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Replies: 46
Views: 20,051
Hmm. What happens when you cuffcompare the...
Hmm. What happens when you cuffcompare the merged GTF files from cuffmerge produced using the different methods? Does Cufflinks produce substantially different assemblies when bias correction +...
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Forum: Bioinformatics
06-01-2012, 03:49 AM
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Replies: 46
Views: 20,051
I'm confused about what you did: are you...
I'm confused about what you did: are you following the protocol from the Cufflinks website (the Nature Protocols one)? If not, can you provide the full sequence of commands that you ran? Cufflinks...
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Forum: Bioinformatics
05-31-2012, 07:04 AM
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Replies: 46
Views: 20,051
Can you please send a small data set to...
Can you please send a small data set to tophat.cufflinks@gmail.com that reproduces this behavior? We can't do much unless you can see what you're seeing (and being able to see it in the debugger...
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Forum: Bioinformatics
05-31-2012, 06:47 AM
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Replies: 46
Views: 20,051
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Forum: Bioinformatics
04-12-2012, 08:22 AM
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Replies: 46
Views: 20,051
Hi francicco,
We've fixed this issue in the...
Hi francicco,
We've fixed this issue in the upcoming release of Cufflinks 1.4.0, which is right around the corner. We've been a little swamped with the release of TopHat 2 and other items, but...
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Forum: Bioinformatics
03-13-2012, 05:36 AM
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Replies: 16
Views: 7,300
Hmm, that's annoying... can you show us how...
Hmm, that's annoying... can you show us how you're running cuffmerge? One limitation of the current version of Cuffmerge is that it doesn't do any of its own ORF prediction. So new isoforms of coding...
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Forum: RNA Sequencing
03-12-2012, 06:44 AM
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Replies: 47
Views: 46,429
DEseq and edgeR (and other tools that test raw...
DEseq and edgeR (and other tools that test raw gene-level counts) assume that the features are the same length. However, if you have any differential splicing or isoform switching going on between...
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Forum: RNA Sequencing
03-12-2012, 06:18 AM
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Replies: 47
Views: 46,429
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Forum: Bioinformatics
03-12-2012, 06:10 AM
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Replies: 16
Views: 7,300
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Forum: Bioinformatics
02-29-2012, 04:31 AM
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Replies: 10
Views: 6,028
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Forum: Bioinformatics
02-28-2012, 04:45 PM
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Replies: 21
Views: 10,454
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Forum: Bioinformatics
02-28-2012, 04:30 PM
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Replies: 5
Views: 2,284
Ariel,
Can you send (to the cufflinks...
Ariel,
Can you send (to the cufflinks support list) us a small test set of data and a GTF that reproduces this problem? I suspect (as you do) that it has to do with differences in how bedTools...
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Forum: Bioinformatics
02-28-2012, 04:23 PM
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Replies: 46
Views: 20,051
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Forum: Bioinformatics
02-28-2012, 04:11 PM
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Replies: 10
Views: 6,028
I'm a bit skeptical about that Cuffdiff run -...
I'm a bit skeptical about that Cuffdiff run - we've compared the lists produced by Cuffdiff against the lists produced by arrays run on *exactly* the same RNA, and found that not only does Cuffdiff...
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Forum: Bioinformatics
02-17-2012, 05:47 AM
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Replies: 5
Views: 4,454
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Forum: Bioinformatics
01-20-2012, 06:23 AM
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Replies: 21
Views: 40,496
I can shed some light on this. We have an...
I can shed some light on this. We have an upcoming protocol paper that describes our recommended workflow for TopHat and Cufflinks that discusses some of these issues.
As turnersd outlined,...
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Forum: Bioinformatics
11-16-2011, 05:24 AM
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Replies: 17
Views: 7,642
I'm still very much involved - I just need to...
I'm still very much involved - I just need to limit my development time to features that directly support my work in the lab I joined. I'm a postdoc in John Rinn's lab, and we use Cufflinks and its...
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