Help@Digital Expression Explorer

See below for resolving common issues and questions.

FAQ

Q) My datasets of interest aren't included in DEE. What should I do?

  1. A) Firstly confirm that the species/accession number combination is correct. Then check whether the sequence data is available from the SRA ftp site. If the dataset has been added >2 months ago, then contact us and we'll have it added to DEE within 1 month.

Q) How do I open zip compressed files?

  1. A) Winzip can uncompress .zip files and is available here for free. Decompression tools are also available from the Apple and Android app store for mobile devices.

Q) What tools are recommended for analyzing RNA-seq count data?

  1. A) There are many options, but we recommend Degust for new users.

Q) How do I load the data into R?

  1. A) We have written an R function that interfaces with the webpage and loads data into R. For more information, read the documentation here
  2. and in txt format here .

Q) Can I load the data directly into my Galaxy history?

  1. A) DEE data can be uploaded manually into Galaxy; direct integration is in development.

Q) My DEE data contains multiple technical replicates, how can I aggregate the counts?

  1. A) Counts can be aggregated in R (recommended) as outlined in our guide. Alternatives include awk or even spreadsheet software (ie. Excel).

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