Count Positive But TPM and FPKM Are Zero

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

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Count Positive But TPM and FPKM Are Zero #130

Open DarioS opened 4 years ago

DarioS commented 4 years ago

There can be results like

gene_id                 transcript_id(s)    length  effective_length    expected_count  TPM FPKM
ENSG00000199631.1   ENST00000362761.1   85.00   0.00                    29.94           0.00    0.00

It's because expected_count doesn't depend on effective_length but TPM and FPKM do. Should it be forced to zero to make the three numeric summaries agreeable?

Wenwen012345 commented 4 years ago

Same problem. Any solution ways?