Embark on arbitrary SRA projects

[olgabot]

This is a far-in-the-future goal, and will probably use https://github.com/maxogden/dat and the bionode toolkits:

• https://github.com/bionode/bionode-sra
• https://github.com/bionode/bionode-sam
• ... more on the bionode page

This is what I would like to be able to do. For example Pollen et al is a paper from fluidigm that performed single-cell RNA seq on a bunch of cell lines. I want to be able to do:

import flotilla
study = flotilla.embark('SRP041736')

And get the data as a flotilla project. This will require a lot of back-end work to run aligners, gene expression and splicing quantifiers, (which could eventually be specified as some kind of config file but just getting a proof of concept working with some known defaults would be amazing), but this would be a HUGE step forward for democratizing biological analysis.

[mlovci]

+1 On Dec 3, 2014 10:41 AM, "Olga Botvinnik" notifications@github.com wrote:

This is a far-in-the-future goal, and will probably use https://github.com/maxogden/dat and the bionode https://github.com/bionode/ toolkits:

• https://github.com/bionode/bionode-sra
• https://github.com/bionode/bionode-sam
• ... more on the bionode https://github.com/bionode/ page

This is what I would like to be able to do. For example Pollen et al http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP041736 is a paper from fluidigm that performed single-cell RNA seq on a bunch of cell lines. I want to be able to do:

import flotilla study = flotilla.embark('SRP041736')

And get the data as a flotilla project. This will require a lot of back-end work to run aligners, gene expression and splicing quantifiers, (which could eventually be specified as some kind of config file but just getting a proof of concept working with some known defaults would be amazing), but this would be a HUGE step forward for democratizing biological analysis.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/flotilla/issues/210.