Question: GEO submission for RNA-seq
0
gravatar for Sadia
2.3 years ago by
Sadia40
Sadia40 wrote:

Hello, one of the requirements to submit RNA-seq data to GEO is processed files which they describe can be:

  1. raw counts of sequencing reads for the features of interest, and/or
  2. normalized abundance measurements, e.g., output from Cufflinks, Cuffdiff, DESeq, edgeR, etc.

Has anyone submitted RNA-seq data before and what format did you submit processed data in? We were considering submitting cufflinks output but there are three different files that are output and I'm not sure which file would be used.

Is there a better format to submit??

rna-seq • 1.5k views
ADD COMMENTlink written 2.3 years ago by Sadia40
1

If I remember correctly genes.fpkm.tracking (something similar) is the one which is more relevant as a processed data.

ADD REPLYlink written 2.3 years ago by poisonAlien2.8k

Could you make sure or can someone else confirm this as well?

ADD REPLYlink written 2.3 years ago by Sadia40

I would say that raw data is preferable, leaving everyone all possible options for analysis.

ADD REPLYlink written 2.3 years ago by WouterDeCoster39k
1

Processed data is requested in addition to raw data.

ADD REPLYlink written 2.3 years ago by genomax67k
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