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?
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.
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?
DESeq2 can produce normalized counts as additional output (see Output options), but to the best of my knowledge it needs at least two conditions.
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.
DESeq2 ‘determines differentially expressed features’. I doubt it can work on a single condition.