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I am new to rnaseq, I am using RNA star to map the genes and count reads per gene. After running the feature counts on RNA Star output, I will like to proceed to the deseq2 for differential gene expression analysis. What files should I use as the input file? is it just gene count files in tabular form by featurecount?
Thank you
If you have a matrix of raw counts directly from featureCounts then this can directly be used for DESeq2 without further modifications, yes. See: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#count-matrix-input
For more in-depth Galaxy-specific help you should ask at their support forum: https://help.galaxyproject.org/