Quickstart: Click here to use our JupyterHub to go from omic-data to publication figures in a minute
Summary: Every paper that is published with sequencing data is supposed to put their data in the SRA. And those data are generated by your tax money, but the crappy part is that everyone uses their own pipeline to generate the results which make it almost impossible to reuse easily. And one day I decided to run >400k raw sequencing data through the same pipeline, and generated an omic matrix for each data layer which everyone can query and go from data to some common publication figures in a minute. The reason I am posting here is to get some feedback from the community to see what are the data layers they want to see. The project is still in the early phase, your comments will be deeply valued and decide on how the project is going to be. Currently, the project only offers transcript counts and allelic read counts.
Related blog posts:
Overview of the project (Intro): A preview of the Skymap project: Extracting allelic read counts and expression profiles of >400,000 public sequencing runs and merging them into simple -omic matrices that can fit into your hard drive
Design rationale of the computational infrastructure (Method) How can a Jupyter notebook extract the expression levels or allelic read counts from > 200,000 sequencing runs in seconds?
You could include
Skymapin place ofIntroducingin the title since that appears to be the name for your project.Points taken, thanks !!
Is there any reason you keep bumping this to the front page? If everyone did this biostars would be a mess, so please use this feature responsibly.
If I am not mistaken, one of the moderators told me that bumping once per day is fine. If that is a problem, maybe you can email me directly to talk over the problem or clarify in the FAQ. Meanwhile, I will stop bumping the post. Hope this help.
I don't know who told you that but IMO that is not fine, not unless you're adding a good amount of content. We don't have the addressed in the FAQ because no one's tried that before.
I am sorry about this.
The post need not be deleted - just don't bump it again unless you're adding content and it gets bumped automatically because of the added content.
I had said that because you had tried to create a new post (with what looked like an attempt to post a tutorial for this tool but I was not certain). It was mainly to make you aware that instead of creating new posts with similar content it is possible to bump a thread up to main page by editing or adding content to the original post. Doing it every day for 2 weeks is not an appropriate use of that feature.
I wonder what organisms will be covered in the project ? As of now I can see Canis familiaris, Danio rerio ,Drosophila, Human and Mouse for RNAseq data. Should I expect any update in the organism list in the future ?
I have all of them. If people ended up using most of the organism other than mouse and human I will upload all of them.
Edit: It's not all per se, I am somewhat concerned about uploading the prokaryotic which are often associated with higher evolution rate, which makes me doubt whether a reference made sense at all.