-estimated_model_file: file containing model parameters. Generated by
-rsem-calculate-expression.
-estimated_isoform_results: file containing isoform expression levels.
-Generated by rsem-calculate-expression.
-theta0: fraction of reads that are "noise" (not derived from a transcript).
-N: number of reads to simulate.
-output_name: prefix for all output files.
-[-q] : set it will stop outputting intermediate information.
+__reference_name:__ The name of RSEM references, which should be already generated by 'rsem-prepare-reference'
+
+__estimated_model_file:__ This file describes how the RNA-Seq reads will be sequenced given the expression levels. It determines what kind of reads will be simulated (single-end/paired-end, w/o quality score) and includes parameters for fragment length distribution, read start position distribution, sequencing error models, etc. Normally, this file should be learned from real data using 'rsem-calculate-expression'. The file can be found under the 'sample_name.stat' folder with the name of 'sample_name.model'. 'model_file_description.txt' provides the format and meanings of this file.
+
+__estimated_isoform_results:__ This file contains expression levels for all isoforms recorded in the reference. It can be learned using 'rsem-calculate-expression' from real data. The corresponding file users want to use is 'sample_name.isoforms.results'. If simulating from user-designed expression profile is desired, start from a learned 'sample_name.isoforms.results' file and only modify the 'TPM' column. The simulator only reads the TPM column. But keeping the file format the same is required. If the RSEM references built are aware of allele-specific transcripts, 'sample_name.alleles.results' should be used instead.
+
+__theta0:__ This parameter determines the fraction of reads that are coming from background "noise" (instead of from a transcript). It can also be estimated using 'rsem-calculate-expression' from real data. Users can find it as the first value of the third line of the file 'sample_name.stat/sample_name.theta'.
+
+__N:__ The total number of reads to be simulated. If 'rsem-calculate-expression' is executed on a real data set, the total number of reads can be found as the 4th number of the first line of the file 'sample_name.stat/sample_name.cnt'.
+
+__output_name:__ Prefix for all output files.
+
+__--seed seed:__ Set seed for the random number generator used in simulation. The seed should be a 32-bit unsigned integer.
+
+__-q:__ Set it will stop outputting intermediate information.