Question: Workflow to store and integrate multiple NGS datasets for easy access and analysis
0
gravatar for urjaswita
22 months ago by
urjaswita80
United States
urjaswita80 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 • 645 views
ADD COMMENTlink written 22 months ago by urjaswita80

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 22 months ago by mark.ziemann1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1830 users visited in the last hour