+A gene's 'length' and 'effective_length' are
+defined as the weighted average of its transcripts' lengths and
+effective lengths (weighted by 'IsoPct'). A gene's abundance estimates
+are just the sum of its transcripts' abundance estimates.
+
+=item B<sample_name.alleles.results>
+
+Only generated when the RSEM references are built with allele-specific
+transcripts.
+
+This file contains allele level expression estimates for
+allele-specific expression calculation. The first line
+contains column names separated by the tab character. The format of
+each line in the rest of this file is:
+
+allele_id transcript_id gene_id length effective_length expected_count TPM FPKM AlleleIsoPct AlleleGenePct [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_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 "[]" are
+optional. They will not be presented if neither '--calc-pme' nor
+'--calc-ci' is set.
+
+'allele_id' is the allele-specific name of this allele-specific transcript.
+
+'AlleleIsoPct' stands for allele-specific percentage on isoform
+level. It is the percentage of this allele-specific transcript's
+abundance over its parent transcript's abundance. If its parent
+transcript has only one allele variant form, this field will be set to
+100.
+
+'AlleleGenePct' stands for allele-specific percentage on gene
+level. It is the percentage of this allele-specific transcript's
+abundance over its parent gene's abundance.
+
+'AlleleIsoPct_from_pme_TPM' and 'AlleleGenePct_from_pme_TPM' have
+similar meanings. They are calculated based on posterior mean
+estimates.
+
+Please note that if this file is present, the fields 'length' and
+'effective_length' in 'sample_name.isoforms.results' should be
+interpreted similarly as the corresponding definitions in
+'sample_name.genes.results'.
+
+=item B<sample_name.transcript.bam, sample_name.transcript.sorted.bam and sample_name.transcript.sorted.bam.bai>
+
+Only generated when --no-bam-output is not specified.
+
+'sample_name.transcript.bam' is a BAM-formatted file of read
+alignments in transcript coordinates. The MAPQ field of each alignment
+is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)), where w is the
+posterior probability of that alignment being the true mapping of a
+read. In addition, RSEM pads a new tag ZW:f:value, where value is a
+single precision floating number representing the posterior
+probability. Because this file contains all alignment lines produced
+by bowtie or user-specified aligners, it can also be used as a
+replacement of the aligner generated BAM/SAM file. For paired-end
+reads, if one mate has alignments but the other does not, this file
+marks the alignable mate as "unmappable" (flag bit 0x4) and appends an
+optional field "Z0:A:!".
+
+'sample_name.transcript.sorted.bam' and
+'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
+indices generated by samtools (included in RSEM package).
+
+=item B<sample_name.genome.bam, sample_name.genome.sorted.bam and sample_name.genome.sorted.bam.bai>
+
+Only generated when --no-bam-output is not specified and --output-genome-bam is specified.
+
+'sample_name.genome.bam' is a BAM-formatted file of read alignments in