TPM quantification (StringTie) of long-read isoforms in TCGA breast tumors and GTEx

StringTie was applied to quantify the expression of long-read isoforms sequenced in TCGA and GTEx samples.

Inputs:

• RNA-seq samples (bam files) from breast cancer samples from TCGA (tumors) and GTEx tissues (healthy controls).
• GTF: full-length isoforms sequenced using PacBio long-read sequencing in breast tumors. See A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer.

Output: tab-delimited files with TPM values for isoforms parsed from StringTie results.

More details: A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer