What is the difference between gene FPKM and transcript FPKM values? Or rather how is FPKM value for gene obtained from FPKM values of transcript. Average is not suitable as only one transcripts may have expression out of several. So what method is used to do so.

Thak you Seidel for showing the way. I have now been able to find the calculation methods.

The general method for calculation of transcript FPKM is explained [here][1].

As I am using Ballgown tool, I found the answer to my question in [supplementary][2] article in one of their papers [Ballgown bridges the gap between transcriptome assembly and expression analysis][3]. The gene FPKM vale calulation is explained under the heading Expression data.

  [1]: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/
  [2]: https://media.nature.com/original/nature-assets/nbt/journal/v33/n3/extref/nbt.3172-S1.pdf
  [3]: https://www.nature.com/articles/nbt.3172