Question: Where/how should processed data be deposited when raw data was already published?
gravatar for TFTF
2.9 years ago by
TFTF30 wrote:

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.

repository reproducibility • 692 views
ADD COMMENTlink modified 2.9 years ago by GenoMax96k • written 2.9 years ago by TFTF30
gravatar for Devon Ryan
2.9 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

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 COMMENTlink written 2.9 years ago by Devon Ryan98k

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

ADD REPLYlink written 2.9 years ago by TFTF30
gravatar for GenoMax
2.9 years ago by
United States
GenoMax96k wrote:

You can use CyVerse.

ADD COMMENTlink written 2.9 years ago by GenoMax96k


ADD REPLYlink written 20 months ago by rlwalls200810
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