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File containing isoform level expression estimates. The first linecontains column names separated by the tab character. The format ofeach line in the rest of this file is:

transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]

Fields are separated by the tab character. Fields within "[]" areoptional. They will not be presented if neither '--calc-pme' nor'--calc-ci' is set.

'transcript_id' is the transcript name of this transcript. 'gene_id'is the gene name of the gene which this transcript belongs to (denotethis gene as its parent gene). If no gene information is provided,'gene_id' and 'transcript_id' are the same.

'length' is this transcript's sequence length (poly(A) tail is notcounted). 'effective_length' counts only the positions that cangenerate a valid fragment. If no poly(A) tail is added,'effective_length' is equal to transcript length - mean fragmentlength + 1. If one transcript's effective length is less than 1, thistranscript's both effective length and abundance estimates are set to0.

'expected_count' is the sum of the posterior probability of each readcomes from this transcript over all reads. Because 1) each readaligning to this transcript has a probability of being generated frombackground noise; 2) RSEM may filter some alignable low quality reads,the sum of expected counts for all transcript are generally less thanthe total number of reads aligned.

'TPM' stands for Transcripts Per Million. It is a relative measure oftranscript abundance. The sum of all transcripts' TPM is 1million. 'FPKM' stands for Fragments Per Kilobase of transcript perMillion mapped reads. It is another relative measure of transcriptabundance. If we define l_bar be the mean transcript length in asample, which can be calculated as

l_bar = \sum_i TPM_i / 10^6 * effective_length_i (i goes through every transcript),

the following equation is hold:

FPKM_i = 10^3 / l_bar * TPM_i.

We can see that the sum of FPKM is not a constant across samples.

'IsoPct' stands for isoform percentage. It is the percentage of thistranscript's abandunce over its parent gene's abandunce. If its parentgene has only one isoform or the gene information is not provided,this field will be set to 100.

'posterior_mean_count', 'pme_TPM', 'pme_FPKM' are posterior meanestimates calculated by RSEM's Gibbssampler. 'posterior_standard_deviation_of_count' is the posteriorstandard deviation of counts. 'IsoPct_from_pme_TPM' is the isoformpercentage calculated from 'pme_TPM' values.

'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound' and'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%credibility intervals for TPM and FPKM values. The bounds areinclusive (i.e. [l, u]).

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