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Forum: Bioinformatics 06-19-2013, 01:44 AM
Replies: 0
Views: 1,279
Posted By amcloon
data inclusion for dispersion estimates in DEseq?

I guess I mostly am asking the DESeq team, ie. Simon Anders, but wanted to put this out there for others doing similar experiments.

I want to make a series of pair-wise comparisons, A vs. B, A...
Forum: Bioinformatics 06-19-2013, 01:38 AM
Replies: 4
Views: 2,029
Posted By amcloon
I'm not sure if you worked out an answer to this...

I'm not sure if you worked out an answer to this yourself, but my observation is that you can set up the count table with either a subset of conditions (just A and B) or all conditions (A, B, C) with...
Forum: Bioinformatics 06-19-2013, 01:18 AM
Replies: 9
Views: 1,992
Posted By amcloon
To view some reads, you don't need Bowtie at all....

To view some reads, you don't need Bowtie at all. If you want to look at your raw sequence reads (rather than the .bam file, which dpryan explained how to view), what you need is just a command like...
Forum: RNA Sequencing 06-18-2013, 09:22 AM
Replies: 10
Views: 3,267
Posted By amcloon
As I said above, what worked for me was changing...

As I said above, what worked for me was changing the way the .gtf file was coded. But still, cuffdiff wasn't the best option for me in the end, even when the gene names showed up. Good luck.
Forum: Bioinformatics 06-18-2013, 02:22 AM
Replies: 9
Views: 1,992
Posted By amcloon
You could see if anyone at your institute has a...

You could see if anyone at your institute has a program like Geneious (sp?) or CLC Genomics workbench and test those (or test a demo version). The programs are expensive and perhaps not as powerful...
Forum: RNA Sequencing 06-18-2013, 01:47 AM
Replies: 10
Views: 3,267
Posted By amcloon
Baoqing, I don't remember, but I might have...

Baoqing,
I don't remember, but I might have meant "-g" and not "-r". in any case, I found that it really matters how your .gtf file is coded. It doesn't just matter that it is .gtf, it also really...
Forum: RNA Sequencing 05-24-2013, 07:40 AM
Replies: 0
Views: 824
Posted By amcloon
DESeq; can I omit timepoints during dispersal estimation?

I have a bacterial timecourse with 2 biological replicates per timepoint. There is a fair bit of variance between my replicates.
I have spent the last few days working with DESeq, and I've been...
Forum: RNA Sequencing 04-30-2013, 06:44 AM
Replies: 5
Views: 1,370
Posted By amcloon
Thanks, Simon, I'll give DESeq a try.

Thanks, Simon, I'll give DESeq a try.
Forum: RNA Sequencing 04-30-2013, 06:15 AM
Replies: 5
Views: 1,370
Posted By amcloon
I didn't do qPCR validation of the second data...

I didn't do qPCR validation of the second data set, but if I do parallel analyses for each set of replicates (at least in the CLC software) I do see up-regulation of a number of known genes within...
Forum: RNA Sequencing 04-29-2013, 08:46 AM
Replies: 5
Views: 1,370
Posted By amcloon
differential gene expression and variance issues

I have 5 time-points with 2 biological replicates (collected and prepared on separate days following exactly the same protocol) of bacteria during starvation-induced development. I've done analysis...
Forum: RNA Sequencing 03-07-2013, 09:45 AM
Replies: 10
Views: 3,267
Posted By amcloon
Not very satisfying possible workaround

Well, I've continued playing around and there are still many things that confuse me, but if you also have this problem (annotations in a .gff file and you want to have an annotated list for cuffdiff)...
Forum: RNA Sequencing 03-06-2013, 06:48 AM
Replies: 10
Views: 3,267
Posted By amcloon
A post-doc and the case of the disappearing gene names (in Cufflinks/cuffdiff)

I've successfully gotten scatter plots, etc. in cummeRbund, but then when I try to actually dig into the data (trying to see if individual transcripts match the patterns we've seen previously with...
Forum: RNA Sequencing 03-01-2013, 07:27 AM
Replies: 3
Views: 1,928
Posted By amcloon
Ah, thank you FJ, that makes sense. So, if I...

Ah, thank you FJ, that makes sense. So, if I interpret that right, the higher the number of threads, the faster it will go, but the more it will monopolize computer resources.
Forum: RNA Sequencing 03-01-2013, 07:24 AM
Replies: 3
Views: 6,140
Posted By amcloon
This was also a concern of mine since I work with...

This was also a concern of mine since I work with a GC-rich species, and it is clear from Aird et al, 2011 (Genome Biology 12:R18) that PCR conditions during library prep can non-uniformly amplify...
Forum: RNA Sequencing 03-01-2013, 07:08 AM
Replies: 3
Views: 1,928
Posted By amcloon
"-p" option in cufflinks, topHat, etc.

Hello,

I'm trying to figure out topHat, cufflinks, etc. and I am getting them to work at the moment (fingers crossed) but I'm trying to understand what I am actually doing. what does the "-p"...
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