GEO submission for RNA-seq

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7.8 years ago

Sadia ▴ 60

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

raw counts of sequencing reads for the features of interest, and/or
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 • 3.2k views

ADD COMMENT • link 7.8 years ago by Sadia ▴ 60

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

ADD REPLY • link 7.8 years ago by poisonAlien ★ 3.2k

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

ADD REPLY • link 7.8 years ago by Sadia ▴ 60

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

ADD REPLY • link 7.8 years ago by WouterDeCoster 47k

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Processed data is requested in addition to raw data.

ADD REPLY • link 7.8 years ago by GenoMax 147k

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