Hi, i’d like to calculate FPKM & RPKM from counts(got from FeatureCounts in Galaxy), how can i do that directly using tools?
Hi @Dr.Lida
Maybe try Cufflinks or FPKM Counts, but these tools use BAM files and gene annotations.
I am not aware about a converter for such operation in Galaxy.
If you after normalized counts, maybe run popular DGE tools, such as edgeR, DESeq2 or limma-voom. You’ll get TPM. You may activate additional outputs, as well.
Kind regards,
Igor
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