Hi, I have realized a de novo annotation of some genes of interest using https://github.com/shenkers/isoscm. I can generate a few different isoforms for a dozen of genes that are of particular interest to me. I end up with a gtf file of my various transcripts.

Could you give me your advice on how to quantify their use in a given alignment? I have already done some Northern Blot and RT-qPCR to identify isoforms and estimate their relative abundance, for a few specific genes.

What I would like to get now for each of my genes is a relative abundance along those lines: in this given gene, transcript x represents y% of all isoforms, plus or minus z%.

I have noticed this listing of quantification software (http://omictools.com/quantification-c354-p1.html) and it is a bit overwhelming to say the least.

I won't use the reference annotation (gtf) or gene regulation (gff) because I work on olfactory genes which are not well annotated. I know Cufflinks is a possible solution, but I want to use my own transcripts (which I checked using IGV).

It seems to me that Salmon might be the easiest solution...

PS: as a last remark, I have masked most of my alignment file since very few genes interest me. Computational requirements won't be an issue here.