I ran TPMCalculator on my RNA-seq data. This was my first time using this package. It seemed to have done without any problems, but I realized that counts of some genes are zero. I performed DEG analysis with Cuffdiff on the same dataset before, and got non-zero FPKMs, such as 100.

My workflow was, Trim-Galore (Adaptor trimming & QC) -> Hisat2 (mapping, with mm10 GTF file) -> SAM tools (conversion to BAM files).

Can anyone tell me what may be wrong ?

Thank you.