TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM).
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8 months ago
Daisuke • 0

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.

RNA-seq TPM • 249 views

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