Quantify the junction abundance?

Question

[lm]

Hi,

I retrieved the TCGA junction, exon, isoform count, and gene level raw counts from TCGA data. For the gene of interest, ex.gene X, there is an splice variant that lacks one specific exon, ex. exon 6, called it X_delta_6 Based on the available data from TCGA that I have, I want to quantify and compare the abundance of gene X and X_delta_6.

There is a study that performed similar analysis for ERBB2-delta16 for TCGA data, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7443881/.

However I am not sure how they perform this analysis based on the description in the method section. Any guidance about it.

Answer 1

[Zhenyu Zhang]

Should you just ask the authors first instead of here?