Question: Workflow to store and integrate multiple NGS datasets for easy access and analysis
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gravatar for urjaswita
2.9 years ago by
urjaswita90
United States
urjaswita90 wrote:

Our lab has a variety of NGS datasets that have been accumulating for many years (RNA-Seq, ChiP-Seq, DNase-Seq etc.) for different conditions and projects. In addition there are many relevant public datasets that are available too (e.g. ENCODE). I was wondering how to best organize and store these datasets so that an integrative analysis can be readily done.

I guess simplest can be that I have respected files for each processed file (e.g. ChiP-Seq peaks, RPKM values for RNA-Seq etc.) for different condition, but then it's difficult to summarize all the data for any new person. Have someone experienced similar issues, and found or developed a useful pipeline to store and integrate multidimensional genomic datasets?

Thanks!

rna-seq chip-seq next-gen ngs • 800 views
ADD COMMENTlink written 2.9 years ago by urjaswita90

Keeping lists of genes in GMT format from each experiment is a lightweight approach. Differential RNA-seq data can be collapsed into rank files which can be analysed using spearman correlation.

ADD REPLYlink written 2.9 years ago by mark.ziemann1.2k
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