Meeting next Monday

[Kevin Rue]

Hi all,

We are planned for a meeting next Monday 18th of November at 2pm. 

Does anyone have suggestions of topics to discuss?

Has anyone applied a technique to their data, and would like to share their results and feedback?

Any new new approach you have read about,but are not sure how to apply?

etc.etc.

Would you prefer to discuss ChIP-seq? RNA-seq? genome assembly? ...?

While we recently mainly used the meeting to help Catherine get started with RNA-seq, I think the meeting would benefit again from more people presenting and sharing their own projects. 

Any volunteers?

Kevin

--
Kévin RUE-ALBRECHT
Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

[Catherine Mooney]

Hi Everyone,

If anyone has had any experience with TopHat-Fusion or SNP detection in RNA-Seq data I'd be really interested to hear about your experience.

Thanks,

Catherine

**********************************************************
Dr Catherine Mooney,
Shields Lab, School of Medicine and Medical Science,
University College Dublin, Ireland.

Phone: +353 1 716 5386

http://bioinformatics.ucd.ie/shields/
http://www.ucd.ie/casl/people/caslpostdocs/drcatherinemooney/

Office address:
2J4, UCD-CASL,
Belfield, Dublin 4, Ireland.
**********************************************************

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[Jai Prakash Mehta]

Hi Catherine,

TopHat-Fusion did not worked out very well for me. It used to produce lots of false positives, though it used to work very well with the example datasets. The only reason that I can think was that our data was 2x35 whereas example datasets were 2x50. 
It requires local BLAST to be set up and depending on your putative fusions and number of samples, it can keep your server engaged for weeks to months. Still a good idea to put it before going for Christmas holidays.

FusionHunter for me worked very well. No false positives and very neat and conclusive results which I was able to validate on a genome browser too.


On SNP calling. mpileup (SAMTOOLS) on sorted indexed BAM will give SNP. The tough part is annotation and finding functional significance which I am still struggling :-( .

Regards
Jai

.

[Yue Fan]

Hi Jai/Catherine,

For variant annotation, we use ANNOVAR, it can use any ucsc genome browser tracks to annotate your variants, there are also functional predicted effect data like SIFT, Polyphen2, etc. 

Regarding fusion detection, we tried a program called Defuse and we got lots of false positive results. It would be interesting to see how this FusionHunt works. 

Thanks. 

Regards

Yue

[Kevin Rue]

Hi all,

We are scheduled to have a meeting today at 2pm in the interactive hub, after the Monday PhD seminar.

However, I  haven't heard of any specific offer of presentation or "journal club" discussion of any article.

Did anyone want to talk/present stuff regarding Catherine's question about "TopHat-Fusion or SNP detection in RNA-Seq data" ?

Kevin