Table 1.

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

transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
comp56_c0_seq1	comp56_c0	3739	3443	637.65	16664.43	7008.23	11.26
comp56_c0_seq2	comp56_c0	3697	3401	4966.34	131393.38	55257.53	88.74
comp62_c0_seq1	comp62_c0	7194	6898	4551.13	59364.09	24965.59	95.54
comp62_c0_seq2	comp62_c0	7076	6778	208.87	2771.95	1165.74	4.46

Transcript_id: Trinity transcript identifier

Gene_id: Trinity component to which the reconstructed transcript was derived.

Length: length of the reconstructed transcript.

Effective length: The mean number of 5′ start positions from which an RNA-Seq fragment could have been derived from this transcript, given the distribution of fragment lengths inferred by RSEM. The value is equal to (transcript_length - mean_fragment_length + 1).

Expected count: number of expected RNA-Seq fragments assigned to the transcript given maximum likelihood transcript abundance estimates.

TPM: transcripts per million

FPKM: number of RNA-Seq fragments per kilobase of transcript effective length per million fragments mapped to all transcripts.

IsoPct: percent of expression for a given transcript compared to all expression from that Trinity component.