Forum: Bioinformatics
06-19-2015, 09:04 AM
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Replies: 8
Views: 8,065
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Forum: Bioinformatics
06-27-2013, 07:37 AM
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Replies: 2
Views: 1,956
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Forum: Bioinformatics
06-21-2013, 04:00 PM
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Replies: 2
Views: 1,956
DEXSeq with experimental variables
Hi,
Can anyone let me know if the formulae displayed below are accurate when trying to account for two different experimental variables (batch and age) with DEXSeq? Also, what does the "I(exon ==...
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Forum: Bioinformatics
05-03-2013, 01:34 PM
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Replies: 1
Views: 2,411
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Forum: Bioinformatics
04-05-2013, 06:52 PM
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Replies: 4
Views: 6,416
Hi chadn737,
1, 2) I will have to look into...
Hi chadn737,
1, 2) I will have to look into the DESeq2 R package - thanks for pointing this out.
3) In general, I would agree with you. Nevertheless, my question regarding the variance filters...
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Forum: Bioinformatics
04-05-2013, 04:40 PM
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Replies: 4
Views: 6,416
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Forum: RNA Sequencing
01-17-2013, 07:15 AM
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Replies: 5
Views: 4,483
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Forum: Bioinformatics
01-10-2013, 04:17 PM
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Replies: 6
Views: 2,337
Even if you do not use Cuffdiff for the DE...
Even if you do not use Cuffdiff for the DE analysis, you can run Cufflinks on your samples to get sample-specific .gtf files. These annotations (which can contain novel transcripts/genes) can be...
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Forum: Introductions
01-03-2013, 02:40 PM
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Replies: 0
Views: 1,267
RNA-Seq optimal depth decision in human
Hi,
I was wondering if there are any new insights that anyone could share on the topic of RNA-Seq read depth. Assuming that the RNA samples are polyA-tail selected, and the sequencing is done with...
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Forum: RNA Sequencing
01-03-2013, 02:25 PM
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Replies: 5
Views: 4,483
Hi malachig,
I was wondering if there are...
Hi malachig,
I was wondering if there are any new insights that you could give me on the topic of RNA-Seq read depth. Assuming that the RNA samples are polyA-tail selected, and the sequencing is...
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Forum: Bioinformatics
11-19-2012, 06:32 AM
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Replies: 15
Views: 25,005
Hi fpenagarican,
Unfortunately, I did not...
Hi fpenagarican,
Unfortunately, I did not receive any relevant answer to my question. Still, I can confirm your results - with Cufflinks (and the corresponding Cuffdiff) v.2.0.0, there were no...
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Forum: Bioinformatics
07-10-2012, 08:30 AM
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Replies: 8
Views: 6,146
Hi Simon,
I do not fully understand your...
Hi Simon,
I do not fully understand your statement regarding RIN. Why did you say that RIN most likely does not influence expression in a linear fashion? Do you have any literature evidence that...
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Forum: Bioinformatics
07-03-2012, 01:21 PM
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Replies: 8
Views: 6,146
Hi,
I read Simon's answer from a few months...
Hi,
I read Simon's answer from a few months ago, but could not find details about covariates in the DESeq manual. The covariates I am interested in accounting for are quantitative and are known to...
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Forum: Bioinformatics
06-19-2012, 02:28 PM
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Replies: 15
Views: 25,005
Hi,
I was wondering if anyone had more...
Hi,
I was wondering if anyone had more thoughts about dejavu2010's comment... It is still not clear to me if Cuffdiff is built to analyze differential expression for groups of biological...
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Forum: RNA Sequencing
05-22-2012, 08:34 AM
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Replies: 3
Views: 3,132
Hi craigb,
Thank you for your post - it was...
Hi craigb,
Thank you for your post - it was useful. I was wondering if you found out anything else about the warning message you mentioned:
Warning: malformed line 1, missing columns
track...
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Forum: RNA Sequencing
05-17-2012, 02:51 PM
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Replies: 0
Views: 1,633
Question about Cufflinks Log Output
Hi,
I was wondering if anyone could help me interpret the following part of Cufflinks' output:
> Map Properties:
> Normalized Map Mass: 284238.81
> Raw Map Mass: 284238.81
> ...
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Forum: Bioinformatics
05-17-2012, 02:29 PM
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Replies: 12
Views: 3,215
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Forum: Bioinformatics
05-17-2012, 02:22 PM
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Replies: 12
Views: 3,215
Hi cedance, did you mean splitting (instead of...
Hi cedance, did you mean splitting (instead of merging) the biological replicates in your post? Is there a standard way of doing this, or did you have to write your own script to get the replicates...
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Forum: Bioinformatics
05-17-2012, 09:58 AM
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Replies: 12
Views: 3,215
Thank you, cedance! The number of sequences for...
Thank you, cedance! The number of sequences for each of our samples is at least 25 million, so I will start mapping each sample individually as a first step. I might go back to mapping all samples...
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Forum: Bioinformatics
05-17-2012, 09:03 AM
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Replies: 12
Views: 3,215
TopHat2 run on individual or multiple samples
Hello,
I am trying to decide what the best approach for running TopHat2 is. We have multiple RNA-Seq samples for two different conditions. Is it preferable to run TopHat2 for each individual...
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Forum: Bioinformatics
04-23-2011, 08:12 PM
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Replies: 4
Views: 3,748
Hi,
Hopefully, this is the right place to...
Hi,
Hopefully, this is the right place to post my question:
I ran TopHat v1.2.0 on single reads (40 ntds) generated with Illumina GA IIx. These were the used options:
tophat --max-multihits...
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Forum: Bioinformatics
12-13-2010, 09:06 AM
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Replies: 8
Views: 6,474
Hi,
It does not seem like anyone had solved...
Hi,
It does not seem like anyone had solved the problem mentioned in this thread, but I am hoping that someone could help me with a similar problem. I am using the latest version of Cufflinks...
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Forum: Bioinformatics
12-08-2010, 12:02 PM
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Replies: 4
Views: 2,513
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Forum: Bioinformatics
12-07-2010, 08:40 AM
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Replies: 38
Views: 21,677
Thank you both for your help!
It would be...
Thank you both for your help!
It would be great if anyone from the Cuffdiff team would be able to comment on how exactly the program decides on differential expression between groups. I am not...
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Forum: Bioinformatics
12-07-2010, 07:54 AM
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Replies: 38
Views: 21,677
Hi Thomas,
Can you be more specific?
...
Hi Thomas,
Can you be more specific?
From the Cuffdiff manual I understand that technical replicates are supported, but not biological replicates. For example, if I have 3 control and 4...
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