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. Author manuscript; available in PMC: 2014 Feb 1.
Published in final edited form as: Nat Protoc. 2013 Jul 11;8(8):10.1038/nprot.2013.084. doi: 10.1038/nprot.2013.084

Table 2.

Example contents of RSEM’s ‘genes.results’ file

gene_id transcript_id(s) length effective_length expected_count TPM FPKM
comp56_c0 comp56_c0_seq1,
comp56_c0_seq2		 3701.73 3405.49 5604 148057.81 62265.76
comp62_c0 comp62_c0_seq1,
comp62_c0_seq2		 7188.74 6892.5 4760 62136.04 26131.33

The gene’s length and effective length are defined as the IsoPct weighted sum of transcript lengths and effective lengths. The gene’s expected counts, TPM, and FPKM are defined as the sum of its transcripts’ expected counts, TPM and FPKM.