More advanced mRNAseq, Sep 28-29, 2015

[ctb]

Suggested topics/titles:

"How to publish your mRNAseq transcriptome and differential expression analysis" "mRNAseq: quality control and evaluation" "mRNAseq: next steps" "So you've got some numbers..."

cc @bluegenes @drtamermansour @camillescott

[camillescott]

note from WiSE workshop: Jane is interested in this

[ctb]

ok @bluegenes @drtamermansour @camillescott time to start planning a bit more --

I'd like to do Meeta's (@mistrm82) limma/edgeR/deseq2 comparison: https://github.com/ngs-docs/msu_ngs2015

and someone could do Asela's (@ajwije) pathway stuff: https://github.com/ngs-docs/150826_pathway_analysis - I didn't get a chance to go through it but got good reports.

Chris Hamm (@butterflyology) had a nice thing on dosage compensation - maybe we can steal some of his code and graphs for other purposes? https://angus.readthedocs.org/en/2015/_static/SLDC-code.html

(all from http://angus.readthedocs.org/en/2015/week3.html).

Other thoughts:

• make space for people to ask questions
• help people adapt edgeR/deseq/pathway analysis to their own data - what should we tell them to bring? htseq-count results?
• hold office hours the week before to help people make sure they're bringing the right thing
• update/cover our annotation pipeline suggestions;
• revisit/summarize old workshops
• talk about what figures/analyses to include in your main manuscript and your supp materials

@bluegenes any suggestions?

[bluegenes]

These seem great.

htseq-count results would be good -- do you guys have a strategy for using htseq-count on de novo transcriptomes? Or what strategy do you usually have people use (i.e. eXpress, rsem, kallisto, salmon, intersectBed?).

On Tue, Sep 1, 2015 at 10:02 AM, C. Titus Brown notifications@github.com wrote:

ok @bluegenes https://github.com/bluegenes @drtamermansour https://github.com/drtamermansour @camillescott https://github.com/camillescott time to start planning a bit more --

I'd like to do Meeta's (@mistrm82 https://github.com/mistrm82) limma/edgeR/deseq2 comparison: https://github.com/ngs-docs/msu_ngs2015

and someone could do Asela's (@ajwije https://github.com/ajwije) pathway stuff: https://github.com/ngs-docs/150826_pathway_analysis - I didn't get a chance to go through it but got good reports.

Chris Hamm had a nice thing on dosage compensation - maybe we can steal some of his code and graphs for other purposes? https://angus.readthedocs.org/en/2015/_static/SLDC-code.html

(all from http://angus.readthedocs.org/en/2015/week3.html).

Other thoughts:

• make space for people to ask questions
• help people adapt edgeR/deseq/pathway analysis to their own data - what should we tell them to bring? htseq-count results?
• hold office hours the week before to help people make sure they're bringing the right thing
• update/cover our annotation pipeline suggestions;
• revisit/summarize old workshops
• talk about what figures/analyses to include in your main manuscript and your supp materials

@bluegenes https://github.com/bluegenes any suggestions?

— Reply to this email directly or view it on GitHub https://github.com/dib-lab/dib-training/issues/6#issuecomment-136796480.

Nuri Teresa Pierce PhD Candidate, Marine Biology NSF GRFP and IGERT Fellow Scripps Institution of Oceanography, UCSD (619) 729-1964 ntpierce@ucsd.edu

[ctb]

eXpress is what people have recommended for de novo.

--t

On Fri, Sep 04, 2015 at 01:09:56PM -0700, Tessa Pierce wrote:

These seem great.

htseq-count results would be good -- do you guys have a strategy for using htseq-count on de novo transcriptomes? Or what strategy do you usually have people use (i.e. eXpress, rsem, kallisto, salmon, intersectBed?).

On Tue, Sep 1, 2015 at 10:02 AM, C. Titus Brown notifications@github.com wrote:

ok @bluegenes https://github.com/bluegenes @drtamermansour https://github.com/drtamermansour @camillescott https://github.com/camillescott time to start planning a bit more --

I'd like to do Meeta's (@mistrm82 https://github.com/mistrm82) limma/edgeR/deseq2 comparison: https://github.com/ngs-docs/msu_ngs2015

and someone could do Asela's (@ajwije https://github.com/ajwije) pathway stuff: https://github.com/ngs-docs/150826_pathway_analysis - I didn't get a chance to go through it but got good reports.

Chris Hamm had a nice thing on dosage compensation - maybe we can steal some of his code and graphs for other purposes? https://angus.readthedocs.org/en/2015/_static/SLDC-code.html

(all from http://angus.readthedocs.org/en/2015/week3.html).

Other thoughts:

• make space for people to ask questions
• help people adapt edgeR/deseq/pathway analysis to their own data - what should we tell them to bring? htseq-count results?
• hold office hours the week before to help people make sure they're bringing the right thing
• update/cover our annotation pipeline suggestions;
• revisit/summarize old workshops
• talk about what figures/analyses to include in your main manuscript and your supp materials

@bluegenes https://github.com/bluegenes any suggestions?

??? Reply to this email directly or view it on GitHub https://github.com/dib-lab/dib-training/issues/6#issuecomment-136796480.

Nuri Teresa Pierce PhD Candidate, Marine Biology NSF GRFP and IGERT Fellow Scripps Institution of Oceanography, UCSD (619) 729-1964 ntpierce@ucsd.edu

---

Reply to this email directly or view it on GitHub:

https://github.com/dib-lab/dib-training/issues/6#issuecomment-137842247

C. Titus Brown, ctbrown@ucdavis.edu