Tool: [Crushing the bureaucracy in bioinformatics] Introducing Skymap-JupyterHub: accessing and utilizing reprocessed expression/ allelic read count profiles from >400,000 sequencing runs made simple
8
gravatar for btsui
3 months ago by
btsui280
UCSD
btsui280 wrote:

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?

GitHub page

Manuscript

tool rna-seq snp chip-seq • 733 views
ADD COMMENTlink modified 29 days ago • written 3 months ago by btsui280
2

You could include Skymap in place of Introducing in the title since that appears to be the name for your project.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax58k

Points taken, thanks !!

ADD REPLYlink written 3 months ago by btsui280
1

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.

ADD REPLYlink written 11 weeks ago by WouterDeCoster34k

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.

ADD REPLYlink written 11 weeks ago by btsui280

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.

ADD REPLYlink written 11 weeks ago by RamRS19k

I am sorry about this.

ADD REPLYlink written 11 weeks ago by btsui280

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.

ADD REPLYlink written 11 weeks ago by RamRS19k

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.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by genomax58k

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 ?

ADD REPLYlink written 29 days ago by Chirag Parsania1.2k

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.

ADD REPLYlink modified 29 days ago • written 29 days ago by btsui280
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