Hello all. I’m using DESeq2 pipeline for DEG trying to analyze 500 RNA-seq samples. As far as know we have input each data for each samples, and its quite hard. My question is can we use single csv file including all samples to run the DEseq2 in galaxy. Any advice will be very valuable. Thank you
you can upload your data by using FTP, and then group each set of samples in list datasets. Have a look to the User Interface and Data Manipulation Galaxy trainings. In case you don’t find a solution that fits your problem in those tutorials, just let me know.
My problem is I have all of RNAseq count data (500 samples) in one excell file. When I use EdgeR pipeline, there is an option whether I want to Use “separate count file” or “Single count matrix”. In that case I Just use “Single count matrix”. But in DESeq2 pipeline, I didnt find this option. Rather it use one file for each sample. It means I have to make 500 csv files to upload. Which will take a lot of effort to separate the file. Thank you very much for your kind answer. I really apreciate your response.
which tool did you use for generating the excel file dataset?
I got the data from TCGA database.