Where/how should processed data be deposited when raw data was already published?
2
2
Entering edit mode
4.2 years ago
TFTF ▴ 30

As part of an accepted paper I would like to share both the code and data files so readers can reproduce my results. The code is easy to share via a public repository (e.g. GitHub). However, I am unsure about how to share the data. This is a computational project, so we use published genomic sequence data, process it (mapping/filtering etc), and analyze. I would like to provide the users with the processed data files prior to the downstream analysis (the downstream analysis can be run using the code I will provide). So my question is:

Where can/should I deposit the processed data files for sharing?

Many public scientific data repositories declare that they only accept new data which has not been published already. But the datasets I use have already been published (at least as raw data, or processed with a different pipeline).

Just to be clear, the motivation here is to save users the need to reprocess the entire raw data, which could require significant effort and computational resources.

reproducibility repository • 941 views
ADD COMMENT
3
Entering edit mode
4.2 years ago

We post the datasets we use for Galaxy trainings (fastq, bam, bigwig, vcf, etc.) to Zenodo. This is generally convenient enough, since it's free.

ADD COMMENT
0
Entering edit mode

Thanks! It does indeed seem to be allowed in Zenodo, and there are also nice features linking to GitHub.

ADD REPLY
1
Entering edit mode
4.2 years ago
GenoMax 117k

You can use CyVerse.

ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 2384 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6