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Search: Posts Made By: Cole Trapnell
Forum: Bioinformatics 06-15-2012, 10:22 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
That's excellent - thanks to you and others in...

That's excellent - thanks to you and others in this thread for the helpful feedback. The official release of 2.0.1 is imminent.
Forum: Bioinformatics 06-15-2012, 10:21 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: RNA Sequencing 06-15-2012, 09:37 AM
Replies: 67
Views: 71,512
Posted By Cole Trapnell
As far as I can tell, both of the "flaws" you...

As far as I can tell, both of the "flaws" you have described are actually misunderstandings on your part about how Cufflinks and Cuffdiff work.

1) FPKM values are inflated beyond a direct...
Forum: Bioinformatics 06-12-2012, 06:30 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 06-11-2012, 04:17 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 06-02-2012, 03:21 PM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 06-02-2012, 03:18 PM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 06-02-2012, 03:15 PM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 06-01-2012, 03:52 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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 +...
Forum: Bioinformatics 06-01-2012, 02:49 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 05-31-2012, 06:04 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 05-31-2012, 05:47 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
Can you try re-running this analysis with...

Can you try re-running this analysis with --min-outlier-p 0 to see if it's the inline model checking that's causing the increase in NOTESTs?
Forum: Bioinformatics 04-12-2012, 07:22 AM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
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...
Forum: Bioinformatics 03-13-2012, 04:36 AM
Replies: 16
Views: 5,671
Posted By Cole Trapnell
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...
Forum: RNA Sequencing 03-12-2012, 05:44 AM
Replies: 47
Views: 43,062
Posted By Cole Trapnell
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...
Forum: RNA Sequencing 03-12-2012, 05:18 AM
Replies: 47
Views: 43,062
Posted By Cole Trapnell
The thread you linked to doesn't show a bug, just...

The thread you linked to doesn't show a bug, just an incorrect use of Cufflinks, as I just noted in that thread.

Regarding use of Cufflinks or RSEM with count-based tools like DEseq or edgeR -...
Forum: Bioinformatics 03-12-2012, 05:10 AM
Replies: 16
Views: 5,671
Posted By Cole Trapnell
As far as I can tell, Cufflinks is working...

As far as I can tell, Cufflinks is working correctly and as described in the manual. As noted above, you want -G, not -g.
Forum: Bioinformatics 02-29-2012, 03:31 AM
Replies: 10
Views: 5,585
Posted By Cole Trapnell
Hmm, it certainly looks OK. Do you have a lot of...

Hmm, it certainly looks OK. Do you have a lot of genes with status FAIL? Where'd you get the GTF?

Also, how did you map the reads?
Forum: Bioinformatics 02-28-2012, 03:45 PM
Replies: 21
Views: 9,467
Posted By Cole Trapnell
This issue has been discussed elsewhere on this...

This issue has been discussed elsewhere on this board. As Nicholas points out, RNA-Seq really isn't reliable for very short transcripts. The reason is that all the fragments that map to these...
Forum: Bioinformatics 02-28-2012, 03:30 PM
Replies: 5
Views: 2,039
Posted By Cole Trapnell
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...
Forum: Bioinformatics 02-28-2012, 03:23 PM
Replies: 46
Views: 18,110
Posted By Cole Trapnell
Just to be clear - this is happening only for the...

Just to be clear - this is happening only for the splicing.diff, promoters.diff (and maybe cds.diff?) files? Note gene_exp.diff or isoform_exp.diff?

Can one or both of you send us (to the support...
Forum: Bioinformatics 02-28-2012, 03:11 PM
Replies: 10
Views: 5,585
Posted By Cole Trapnell
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...
Forum: Bioinformatics 02-17-2012, 04:47 AM
Replies: 5
Views: 4,153
Posted By Cole Trapnell
A note about small transcripts and high FPKM: The...

A note about small transcripts and high FPKM: The reason you're seeing this is that with a very small transcript, the fragments that map to it have to be short (at least as short as the transcript),...
Forum: Bioinformatics 01-20-2012, 05:23 AM
Replies: 21
Views: 35,344
Posted By Cole Trapnell
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,...
Forum: Bioinformatics 11-16-2011, 04:24 AM
Replies: 17
Views: 6,680
Posted By Cole Trapnell
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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