Is there a tool that generates FPKM counts of genes automatically?

Hello everyone!

I am working with RNA-seq data of several human samples. I have been able now to obtain successfully a bam file from my samples after alignment with RNASTAR tool, and also obtained read counts with FeatureCounts tool.

However, now I have a problem with obtaining a normalized value for said reads that I can use to compare between genes within the same sample and among samples.

Regarding this topic I have two questions:

  • Is there a tool to obtain gene FPKM counts automatically? I know the “FPKM count tool exists” however it only gives me FPKM values per transcript (ENST code in ENSEMBL) and not per gene (ENSG code). Is there a different tool that can allow me to obtain FPKM/gene?

  • For data normalization would it be better to use another type of count normalization different than FPKM?

Thank you very much in advance,


Hi @Coral

Please see the End-to-End tutorials here, then let us know if you have any followup questions → Transcriptomics / Tutorial List

And, some extra help about formatting your own data for use with Bioconductor tools → FAQ: Extended Help for Differential Expression Analysis Tools

Hope this helps! :slight_smile: