Meeting 27.05

[Tom]

Dear group,

Peadar is talking tomorrow at the sequencing meeting about the seq conference he recently attended.

2 pm in the Interactive Hub (or seminar room 2), you are all very welcome.

This will be the last sequencing meeting organised by me since I will write my thesis from home (Austria).

Regards,

Tom

[Adam Dinan]

Tom, I think I speak for us all when I say that you've done a fantastic job organising these meetings and I can only hope one or two of the rest of us will be as dedicated to keeping them going in future. Thanks!

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[Peadar O'Gaora]

Hi Tom (and all),

It turns out I won't be able to do it today - sorry for the late notice. I'm happy to do it next time though.

I would also endorse what Adam said - well done on organising this group and good luck with the thesis writing.

All the best,
Peadar

On 26 May 2013 23:32, Tom <thomas....@gmail.com> wrote:

--

[Karsten Hokamp]

Hi all,

Since today's slot has just freed up I could give a short presentation on a conundrum regarding absolute and differential gene expression from RNA-seq data that I am facing.

Might help bouncing a few ideas around...

Anybody interested?

Karsten

[Tom]

Hi everybody,

thank you very much. 

Karsten, it would be great to hear about absolute and differential gene expression.

See you in a while,

Tom

[Paul McGettigan]

Hi Karsten,

Here are the papers from the Burge and Young groups in MIT about transcriptional amplification and c-MYC

Loven J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, Young RA. (2012). Revisiting global gene expression analysis.  Cell 151, 476-482. (Primer).
 
Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA. (2012). Transcriptional Amplification in Tumor Cells with Elevated c-Myc.Cell 151, 56-67.


..also a paper on GC-content normalization for RNA-seq
http://www.biomedcentral.com/1471-2105/12/480

-Paul

On 27/05/2013 08:35, "Karsten Hokamp" <kho...@gmail.com> wrote:

Hi all,

Since today's slot has just freed up I could give a short presentation on a conundrum regarding absolute and differential gene expression from RNA-seq data that I am facing.
Might help bouncing a few ideas around...
Anybody interested?

Karsten


On Mon, May 27, 2013 at 8:08 AM, Peadar O'Gaora <pog...@gmail.com> wrote:

Hi Tom (and all),

It turns out I won't be able to do it today - sorry for the late notice. I'm happy to do it next time though.

I would also endorse what Adam said - well done on organising this group and good luck with the thesis writing.

All the best,
Peadar



On 26 May 2013 23:32, Tom <thomas....@gmail.com> wrote:

Dear group,

Peadar is talking tomorrow at the sequencing meeting about the seq conference he recently attended.

2 pm in the Interactive Hub (or seminar room 2), you are all very welcome.

This will be the last sequencing meeting organised by me since I will write my thesis from home (Austria).

Regards,
Tom

--
Dr. Paul McGettigan
Reproductive Biology Cluster
Room 223A
Veterinary Sciences Centre
University College Dublin
Dublin 4
Ireland

tel: 01 716 6229
email: paul.mc...@ucd.ie

[Tom]

The filtering of low expressed counts we discussed about is described here:

http://arxiv.org/abs/1302.3685 

[Yue Fan]

Thanks! Thomas.

Yue

On 27 May 2013, at 16:42, Tom <thomas....@gmail.com> wrote:

The filtering of low expressed counts we discussed about is described here:

http://arxiv.org/abs/1302.3685 

[PubCrawler Administrator]

Hi all,

Attached are the slides from my presentation.

I figured out that Wagner's TPM formula (which they claim to have 'introduced' in 2012), is essentially the same as Li's from 2009. Notation is a bit different but it gives exactly the same results.

Still puzzled why it does so bad in the hypothetical case.

Karsten

Best regards,

        Karsten

--
Karsten Hokamp, Ph.D.
PubCrawler Administrator
Genetics Department, Trinity College Dublin

[Tom]

Hi all, 

thanks Karsten for the slides.

Regarding the normalization issues, we did not discuss one thing: the library size is not clearly defined. 

In Cufflinks e.g. it is the total read count from the whole library as far as I know. In DEseq / edgeR, according to that recent example paper, the counts from htseq-count are read in, but the unmapped reads etc are discarded before normalizing. Which reduces the library size quite a bit in some cases. 

Regards,

Tom