EGA Download Client: authorized datasets

Hi,
I have tried to use the Download Client to download an authorized dataset from EGA. I set up my EGA login and password in the Galaxy Preferences menu. I tried to use DESeq2 tool but in the “count file” section I read "(unavailable) EGA Download Client: authorized datasets. Why?

Thanks
Barbara

Hi @Barbara_Mandriani,
have you uploaded the count table into Galaxy? If yes, click at the name of this dataset in Galaxy history and check the datatype (format: text_string_to_check). Does it say tabular? If the datatyep (format) is anything but tabular, e.g., ‘data’ or ‘txt’, change it to tabular by clicking at Edit Attributes (pencil icon) > Datatypes tab in the middle window > select ‘tubular’ in the pull-down menu.
Just in case: you can import data from a remote site into Galaxy directly using URL. Copy the URL on the remote site, usually with right mouse click > copy YRL or link, and paste it into Galaxy Upload menu, Paste/Fetch data section.
Kind regards,
Igor

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Hi Igor,
thanks a lot for your reply.
I have another question about the data normalization in DESeq2. I have a matrix of gene counts from 30 samples belonging to the same group. I don’t want to get DE genes obviously. I just need to normalised these counts. Is there a way to do this in DESeq2 without the need to specify two conditions?

Hi @Barbara_Mandriani
DESeq2 can produce normalized counts as additional output (see Output options), but to the best of my knowledge it needs at least two conditions.
Kind regards,
Igor

Hi Igor,
I know DESeq2 works well with two conditions. I would like to know if DESeq can also work with one condition and if yes, how I can do this.
Thanks

Hi @Barbara_Mandriani
DESeq2 ‘determines differentially expressed features’. I doubt it can work on a single condition.
Kind regards,
Igor

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