TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM).
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 ?
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