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Forum: RNA Sequencing 04-22-2016, 12:32 PM
Replies: 0
Views: 1,819
Posted By aliceb
Should I sequence un-replicated blocks in RNAseq?

Hi all,

I am designing a new experiment to sequence transcriptomes from wasps. I have 3 treatment "environments" and 4 replicate populations in each (kept separate throughout), for a total of 12...
Forum: Bioinformatics 11-20-2014, 06:32 AM
Replies: 6
Views: 1,523
Posted By aliceb
Ah, thank you! I knew I was missing something in...

Ah, thank you! I knew I was missing something in the results :)
Forum: Bioinformatics 11-20-2014, 05:40 AM
Replies: 6
Views: 1,523
Posted By aliceb
Ah yes, that has much more overlap with the...

Ah yes, that has much more overlap with the unblocked design than the other two.

Thanks very much!
Forum: Bioinformatics 11-20-2014, 05:17 AM
Replies: 6
Views: 1,523
Posted By aliceb
Thanks for the quick response! Yes, I think...

Thanks for the quick response!

Yes, I think I've tried that using: "design= ~ sel.line + sel.line:block"

However, I'm worried that I'm not correctly setting up my design. I have also tried...
Forum: Bioinformatics 11-20-2014, 04:27 AM
Replies: 6
Views: 1,523
Posted By aliceb
DESeq2 with nested design?

Hi all,

Is is possible to use a nested model in DESeq2 or EdgeR??

I have 3 treatments (evolution lines), but each treatment was performed in 4 replicate lines.

My experimental design is...
Forum: Bioinformatics 09-11-2014, 06:01 AM
Replies: 12
Views: 5,156
Posted By aliceb
Yes, I did think of that. But I have now been...

Yes, I did think of that. But I have now been able to get 99% hits on a dataset that crashes against the Anopholes core genes. It seems like there should be some hits there (I am working with a...
Forum: Bioinformatics 09-07-2014, 11:13 PM
Replies: 12
Views: 5,156
Posted By aliceb
Hi all, This is an old thread, but I'm...

Hi all,

This is an old thread, but I'm getting a similar error with CEGMA v2.5. It's not happening all the time - I ran the test data just fine, the test proteins against my data ok, and my data...
Forum: Sample Prep / Library Generation 01-08-2014, 11:49 PM
Replies: 12
Views: 11,497
Posted By aliceb
Thanks for the reply! We're working with wasps...

Thanks for the reply! We're working with wasps that can be grown up, but high numbers will be a bit of a struggle. And as they're variable, sexual populations there will certainly be information...
Forum: Sample Prep / Library Generation 01-08-2014, 12:39 PM
Replies: 12
Views: 11,497
Posted By aliceb
Hi all, To dredge up an old question again,...

Hi all,

To dredge up an old question again, I was wondering if I could get an opinion on a pooling / not pooling design.

First, I understand that I want biological replicates! But is it better...
Forum: Bioinformatics 11-07-2012, 04:20 PM
Replies: 5
Views: 1,277
Posted By aliceb
Hi Anna, I'm afraid I haven't used bwa, but...

Hi Anna,

I'm afraid I haven't used bwa, but we see similar results with bowtie2 (although not quite to the same extent as you).

When we recover counts from our sam file (we're using...
Forum: Bioinformatics 11-07-2012, 02:16 PM
Replies: 5
Views: 1,277
Posted By aliceb
Hi Anna, It sounds like some of your reads...

Hi Anna,

It sounds like some of your reads are mapping to more than one place. This way they would be reported more than once in your counts.

How are you doing the mapping?

-Alice
Forum: Bioinformatics 05-08-2012, 06:41 PM
Replies: 3
Views: 3,142
Posted By aliceb
Trinity vs Mira /de novo assembly

Hi all,

I'm keen to see how others are getting on with de novo assemblies, particularly with Trinity. It's interesting to me that their Nat. Biotechnology paper doesn't mention Mira, and I was...
Forum: Bioinformatics 11-13-2011, 12:12 PM
Replies: 21
Views: 15,328
Posted By aliceb
Hmmm, it seems like some people are having...

Hmmm, it seems like some people are having trouble getting a cuffmerge file to run in later analyses, while others are having trouble getting cuffmerge to execute at all.

I'm getting this...
Forum: Bioinformatics 11-12-2011, 06:00 PM
Replies: 21
Views: 15,328
Posted By aliceb
Header problems... cuffmerge

Hi all,

I'm getting a header error when using Cuffmerge, and I was wondering if anyone has been dealing with this recently (I'm using cufflinks v1.1.0/Sept 2011). I'm getting the following error:...
Forum: Sample Prep / Library Generation 08-14-2011, 04:53 PM
Replies: 12
Views: 2,578
Posted By aliceb
Have you had any luck? I might worry less...

Have you had any luck?

I might worry less about the total RNA you have and more about how much mRNA you can squeeze out of it. I've had better results from the oligotex mRNA purification kit,...
Forum: 454 Pyrosequencing 09-02-2010, 08:56 PM
Replies: 10
Views: 5,816
Posted By aliceb
Hi again- thanks for the help. You're post is...

Hi again- thanks for the help. You're post is really useful, particularly the graphic to illustrate the contig/isotig/isogroup business. I'm sending a couple of screenshots from geneious and tablet....
Forum: 454 Pyrosequencing 08-30-2010, 01:34 PM
Replies: 10
Views: 5,816
Posted By aliceb
Thanks for the reply.. I thought I understood...

Thanks for the reply.. I thought I understood this contig/isotig/isogroup business, but maybe not...

My problem is that there are contigs that are exactly identical- many base pairs overlap and...
Forum: 454 Pyrosequencing 08-29-2010, 07:04 PM
Replies: 10
Views: 5,816
Posted By aliceb
Hi all- I think I'm having similar problems with...

Hi all- I think I'm having similar problems with alignments using the cDNA setting for de novo assembly.

(1) when I put the contigs resulting from Newbler into Geneious, I find several hundred of...
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