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sr320 / paper-pano-go

Draft manuscript describing Panopea gonad transcriptome
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super interested (SNPs section?) #5

Closed paolabatta closed 8 years ago

paolabatta commented 8 years ago

Hola Steven: I hope you had a good trip back, I had a great time in CT, I arrived last night and I'm getting back into the swing of things. I will be interested in collaborating, maybe with the SNP section or with CPG. However I want to make sure I understand how it all works. I will be submitting my text and methodology to this repository. And so far you had put in examples of what type of text and methods you want to include in this manuscript? I look forward to getting some feedback and guidance on the direction of this manuscript.

Saludos!

sr320 commented 8 years ago

Hola Paola! Yes- that is the idea, that we would just collaborate using this repository. We would commit new material as generated. Could either edit online via GitHub or locally, making sure to commit and sync :+1: .

I experimented a bit today with the pull request model (we might have covered that after you left). I think that might be too complicated for most so I will add interested folks as collaborators so the can edit without pull requests and merges.

JaviRobles commented 8 years ago

Hello! Also I am interested, I share the idea of Paola. I like to read and learn more about all this new landscape for me; if you could provide me essential articles for all this, it would be helpful. I will also be on the lookout for what happens to it.

Greetings!

sr320 commented 8 years ago

One good place to start with SNPs is to take SAM file from Trinity assembly - https://github.com/sr320/paper-pano-go/wiki/Raw-Data#trinity-output

and use Samtools to create VCF file. See http://www.htslib.org/doc/samtools.html

paolabatta commented 8 years ago

Im on it!

Dra.Paola G. Batta Lona Departamento de Biotecnologia Marina CICESE pbatta@cicese.mx Tel:+52 (646) 1750500, ext 27164 Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, B.C. Mexico,

On Sat, Oct 31, 2015 at 6:57 AM, Steven Roberts notifications@github.com wrote:

One good place to start with SNPs is to take SAM file from Trinity assembly - https://github.com/sr320/paper-pano-go/wiki/Raw-Data#trinity-output

and use Samtools to create VCF file. See http://www.htslib.org/doc/samtools.html

— Reply to this email directly or view it on GitHub https://github.com/sr320/paper-pano-go/issues/5#issuecomment-152738463.

lacroix54 commented 8 years ago

Hi Steven,

I'm interested too, so, i want to work with the part of annotation. But, first I need to integrate all that you taught us, and i plan to work with Dr. Miguel and Dra. Fabiola, and here i'll be commenting the progress and my queries.

Saludos, Carmen

sr320 commented 8 years ago

I will go ahead and close this specific issue, but please add new issue as questions arise.. :fire_engine: