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Forum: Bioinformatics 08-06-2015, 04:48 AM
Replies: 4
Views: 730
Posted By Sciurus
Yes, I am using Notepad++ but I have no other...

Yes, I am using Notepad++ but I have no other explanation for what went wrong before...
Forum: Bioinformatics 08-06-2015, 04:32 AM
Replies: 4
Views: 730
Posted By Sciurus
Thanks for the suggestion! Strangely enough,...

Thanks for the suggestion!

Strangely enough, I retyped the whole command and now it runs even though everything is still the same.

Maybe there was some weird formation thing going on in my...
Forum: Bioinformatics 08-06-2015, 03:51 AM
Replies: 4
Views: 730
Posted By Sciurus
Cuffdiff error???

Hi everybody,

I keep getting the same error when trying to run cuffdiff:
number of labels must match number of conditions.

I have two groups/ treatments with 4 replicates each.

Now, I've...
Forum: Bioinformatics 06-22-2015, 05:34 AM
Replies: 0
Views: 1,227
Posted By Sciurus
How to use DANPOS2 with ATAC Seq data?

Hi smart folks out there :-)

I was wondering about the analysis of ATAC Seq data and specifically about the step using DANPOS2. It has been developed to analyse MNAse Seq data, right?

But...
Forum: Bioinformatics 06-15-2015, 03:51 AM
Replies: 22
Views: 21,048
Posted By Sciurus
Thanks a lot! :) Now, when using macs2 is it...

Thanks a lot! :)

Now, when using macs2 is it correct to set the offset of 75bp, that was used by Buenrostro et al. with
--nomodel --shift 37 --extsize 37?
Forum: Bioinformatics 06-09-2015, 05:46 AM
Replies: 22
Views: 21,048
Posted By Sciurus
Thanks for your replies! But in order to...

Thanks for your replies!

But in order to work with macs2, I'd need to use Python or is there another way of implementing it in linux?

I don't know how to program with Python, btw. ;-)
Forum: Bioinformatics 06-03-2015, 04:39 AM
Replies: 22
Views: 21,048
Posted By Sciurus
Thanks a lot! :)

Thanks a lot! :)
Forum: Bioinformatics 06-02-2015, 01:46 AM
Replies: 22
Views: 21,048
Posted By Sciurus
ATAC Seq data analysis

Hi everybody,

We have recently done our first ATAC Seq project in our lab and my task is analysing the data. But since I am quite new to bioinformatics, I was wondering whether somebody here has...
Forum: Bioinformatics 04-15-2014, 02:59 AM
Replies: 5
Views: 2,188
Posted By Sciurus
So, I am still struggling with this nested...

So, I am still struggling with this nested design. If you would be so kind as to have a look here, I'd very much appreciate any help I can get! :-)
...
Forum: Bioinformatics 04-15-2014, 02:38 AM
Replies: 11
Views: 2,453
Posted By Sciurus
Dear Mr Anders, Thank you for your...

Dear Mr Anders,

Thank you for your suggestion. I have since switched to using DESeq2, however, I am still having trouble with the nested design.

My data.frame looks like this:

> ExpDesign...
Forum: Bioinformatics 04-07-2014, 06:27 AM
Replies: 5
Views: 2,188
Posted By Sciurus
Okay, thank you! I ran both options and will...

Okay, thank you! I ran both options and will discuss with my supervisor when I get a chance.
Forum: Bioinformatics 04-07-2014, 04:53 AM
Replies: 5
Views: 2,188
Posted By Sciurus
Thank you! Yes, that is what I have been...

Thank you!

Yes, that is what I have been wondering: What makes sense and is statistically legitimate to do.
What would 3-way-ineraction mean in terms of statistical power and meaning I can draw...
Forum: Bioinformatics 04-07-2014, 01:33 AM
Replies: 5
Views: 2,188
Posted By Sciurus
How do I analyze double nested design? (DESeq2)

Hi everybody,

I am currently analysing an RNAseq eperiment I ran on recombinant inbred lines.

So far I have used DESeq but because my design is somewhat complicated and I couldn't do the proper...
Forum: Bioinformatics 04-02-2014, 12:39 AM
Replies: 11
Views: 2,453
Posted By Sciurus
Hey guys, I have a similar problem, however...

Hey guys,

I have a similar problem, however my data is a double nested design (if that makes sense, I'm new to analysing RNAseq data).

Which means that I have 24 samples:
12 are parents (as...
Forum: Illumina/Solexa 02-20-2014, 05:11 AM
Replies: 3
Views: 1,989
Posted By Sciurus
I'd be interested in that too! Anybody any idea?...

I'd be interested in that too! Anybody any idea? :-)
Forum: Sample Prep / Library Generation 01-29-2014, 07:18 AM
Replies: 5
Views: 2,797
Posted By Sciurus
Okay, thanks! So, you'd say it's DNA...

Okay, thanks! So, you'd say it's DNA contamination?
Forum: Sample Prep / Library Generation 01-29-2014, 07:10 AM
Replies: 5
Views: 2,797
Posted By Sciurus
I didn't do DNA-free treatment yet. But I hadn't...

I didn't do DNA-free treatment yet. But I hadn't done before either when the results were good.
I was suggested that the RNA hadn't completely resolved in the buffer. Can that be?
Forum: Sample Prep / Library Generation 01-29-2014, 06:06 AM
Replies: 5
Views: 2,797
Posted By Sciurus
Need help interpreting these weird Bioanalyzer results

Hi everybody,

Today, I extracted RNA from plant material, which I want to - eventually - sequence. For quality check I ran them on the Bioanalyzer as I have done several times with the same type...
Forum: Sample Prep / Library Generation 01-23-2014, 01:35 AM
Replies: 5
Views: 4,141
Posted By Sciurus
Thanks, guys! Yes, that's what we concluded in...

Thanks, guys!
Yes, that's what we concluded in the end too - overamplification of the library due to too much starting material + too many pcr cycles.

I am redoing the library.
Forum: Sample Prep / Library Generation 12-11-2013, 05:28 AM
Replies: 41
Views: 25,647
Posted By Sciurus
Okay, thanks! Our technician suggested running...

Okay, thanks!
Our technician suggested running a NuSieve gel and re-purifying with beads.
I'm not entirely sure if that will help any but I'll probably try and then re-do the libraries if that...
Forum: Sample Prep / Library Generation 12-10-2013, 06:33 AM
Replies: 41
Views: 25,647
Posted By Sciurus
Thank you! So, this means that I would have...

Thank you!

So, this means that I would have to do a whole new library prep or can I re-fragment these samples?

I used the in-line controls for end-repair, a-tailing and ligation but as far as I...
Forum: Sample Prep / Library Generation 12-10-2013, 05:49 AM
Replies: 41
Views: 25,647
Posted By Sciurus
Maybe here somebody has seen something similar...

Maybe here somebody has seen something similar like my results from the BioAnalyzer run following RNA library prep (and pcr) and can tell me where the huge peak comes from and how to proceed now?
Forum: Sample Prep / Library Generation 12-10-2013, 04:51 AM
Replies: 5
Views: 4,141
Posted By Sciurus
Bioanalyzer: What are these huge fragments (after Illumina TruSeq RNA sample prep)?

Hi everybody,

This has been my second time doing a library prep using total RNA from plants. I used the Illumina TruSeq RNA sample prep kit v2.
Last time, everything worked all fine but this time...
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