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Search: Posts Made By: lpachter
Forum: Bioinformatics 09-09-2015, 09:10 AM
Replies: 4
Views: 1,878
Posted By lpachter
You need to be careful in comparing genes within...

You need to be careful in comparing genes within a single sample, especially if you intend to argue for a "statistically significant" difference. In the absence of replicates you will be unable to...
Forum: RNA Sequencing 08-17-2015, 04:17 PM
Replies: 2
Views: 2,053
Posted By lpachter
If you're quantifying with kallisto you may want...

If you're quantifying with kallisto you may want to take a look at sleuth (http://pachterlab.github.io/sleuth/)
Forum: RNA Sequencing 09-05-2013, 12:20 AM
Replies: 11
Views: 12,613
Posted By lpachter
Its tempting to think that how one counts doesn't...

Its tempting to think that how one counts doesn't matter (for differential expression purposes), but here I argue that it does:
...
Forum: Bioinformatics 03-12-2013, 07:39 AM
Replies: 24
Views: 16,290
Posted By lpachter
Dear Zaki, You ask an excellent question....

Dear Zaki,

You ask an excellent question. This paper answers it in detail:
http://www.nature.com/nbt/journal/v31/n1/abs/nbt.2450.html
Lior
Forum: Bioinformatics 12-12-2012, 03:30 AM
Replies: 52
Views: 83,789
Posted By lpachter
Please see Figure 1 of...

Please see Figure 1 of http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.2450.html#/figure



Please see Figure 3 of ...
Forum: Bioinformatics 06-30-2012, 02:38 PM
Replies: 15
Views: 5,300
Posted By lpachter
Simon is correct that replicates are necessary....

Simon is correct that replicates are necessary. However his comment that data without replicates is useless is an exaggeration, and the idea that published papers without replicates are an...
Forum: RNA Sequencing 05-22-2012, 12:36 PM
Replies: 16
Views: 5,337
Posted By lpachter
That is correct.

That is correct.
Forum: RNA Sequencing 05-15-2012, 10:19 AM
Replies: 16
Views: 5,337
Posted By lpachter
It is possible, although not ideal. Since one can...

It is possible, although not ideal. Since one can assume that most genes are not differential expressed, the control and single treatment can be viewed as biological replicates for the majority...
Forum: RNA Sequencing 05-15-2012, 09:36 AM
Replies: 16
Views: 5,337
Posted By lpachter
"If you present cuffdiff with a single control...

"If you present cuffdiff with a single control and a single treatment sample, it cannot estimate biological variation and will assume it to be zero"

This statement is not correct. Cuffdiff is...
Forum: RNA Sequencing 04-22-2012, 02:45 PM
Replies: 47
Views: 45,779
Posted By lpachter
I'd like to point out that Cole's example is not...

I'd like to point out that Cole's example is not only showing that DESeq and edgeR's assumption of features being the same length is problematic because it might lead to a canceling out that leads to...
Forum: Bioinformatics 05-12-2011, 09:00 PM
Replies: 8
Views: 3,060
Posted By lpachter
Just wanted to let you know that Cufflinks 1.0...

Just wanted to let you know that Cufflinks 1.0 has a completely revamped approach to DE that models over-dispersion of counts at the transcript level and we'll be curious to know how it performs on...
Forum: Bioinformatics 03-18-2011, 12:09 PM
Replies: 34
Views: 35,137
Posted By lpachter
Simon, I agree that its fantastic that the...

Simon,
I agree that its fantastic that the DESeq paper is already published:
http://genomebiology.com/2010/11/10/R106
However I believe it was used by many people long before it appeared in print...
Forum: RNA Sequencing 02-10-2011, 04:15 AM
Replies: 28
Views: 13,136
Posted By lpachter
The reason for excessive transcripts is that in...

The reason for excessive transcripts is that in genes with low coverage, Cufflinks will likely predict multiple disjoint transcripts- that is in fact the only thing it can do because it is not a gene...
Forum: Bioinformatics 01-30-2011, 07:38 AM
Replies: 5
Views: 14,405
Posted By lpachter
Cufflinks currently divides multi-reads (i.e....

Cufflinks currently divides multi-reads (i.e. reads that map to multiple locations) uniformly in calculating expression values. This is not correct, however it is worth pointing out that...
Forum: RNA Sequencing 01-30-2011, 07:30 AM
Replies: 25
Views: 6,566
Posted By lpachter
Thats definitely of interest to us- I'd really...

Thats definitely of interest to us- I'd really like feedback on how well this works and any suggestions you may have on optimizing such a strategy.
Lior (tophat.cufflinks@gmail.com)
Forum: Bioinformatics 01-30-2011, 07:28 AM
Replies: 14
Views: 7,457
Posted By lpachter
Paired end reads are much better for RNA-Seq,...

Paired end reads are much better for RNA-Seq, both for assembly, and also for quantification. There are a number of reasons:
0. As already alluded to on this thread, paired-end reads improve...
Forum: Bioinformatics 01-20-2011, 01:48 PM
Replies: 2
Views: 2,461
Posted By lpachter
This problem is most likely being caused by...

This problem is most likely being caused by polymerase run off on the 3' end of the PHF23 gene.

It is possible, in principle, to identify two distinct genes from such data if the coverage is...
Forum: RNA Sequencing 12-01-2010, 10:07 AM
Replies: 28
Views: 13,136
Posted By lpachter
Dear RCJ, Thanks for attaching the MA plot....

Dear RCJ,

Thanks for attaching the MA plot. Do you recall what version of Cuffdiff you were running? And also whether you compared on the same gene sets? Which organism was this from? It would...
Forum: Bioinformatics 11-15-2010, 08:08 AM
Replies: 3
Views: 2,509
Posted By lpachter
Greg, to answer your last question: tophat uses...

Greg, to answer your last question: tophat uses bowtie as the engine for its read -> genome mapping as part of the algorithm for finding spliced reads. Cufflinks in turn can use the tophat...
Forum: RNA Sequencing 10-06-2010, 03:06 PM
Replies: 24
Views: 15,807
Posted By lpachter
Regarding baySeq, I am not an author on that...

Regarding baySeq, I am not an author on that software so I cannot speak for the details of it. I just mentioned it because it seemed like they do a lot of things right on a lot of aspects of...
Forum: RNA Sequencing 10-06-2010, 08:49 AM
Replies: 24
Views: 15,807
Posted By lpachter
Hi Hypatia, From my current reading of the...

Hi Hypatia,

From my current reading of the literature, it seems to me that baySeq may be a good solution for you right now:
http://www.biomedcentral.com/1471-2105/11/422/

Regarding Cufflinks,...
Forum: Bioinformatics 09-28-2010, 09:50 AM
Replies: 4
Views: 3,557
Posted By lpachter
Dear Uwe, We have just released Cufflinks...

Dear Uwe,

We have just released Cufflinks 0.9 which addresses some of the issues you wrote about, and we would appreciate any feedback.
Forum: RNA Sequencing 09-28-2010, 09:49 AM
Replies: 5
Views: 5,201
Posted By lpachter
Dear Claudia, Cuffdiff can be used to test...

Dear Claudia,

Cuffdiff can be used to test for differential expression, and you may wish to try it. In particular, the new version can be used with replicates and also supports bias correction...
Forum: Bioinformatics 08-24-2010, 04:50 AM
Replies: 5
Views: 3,279
Posted By lpachter
Yes, you can add the FPKM for individual...

Yes, you can add the FPKM for individual transcripts in a gene to get an overall FPKM.
Forum: Bioinformatics 08-05-2010, 04:04 AM
Replies: 23
Views: 24,742
Posted By lpachter
@poisson200: You are absolutely right that it is...

@poisson200: You are absolutely right that it is desirable to perform differential expression at the transcript level, possibly allowing for more general assumptions about the relationship between...
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