+**Format of the header line**: Each simulated read's header line encodes where it comes from. The header line has the format:
+
+ {>/@}_rid_dir_sid_pos[_insertL]
+
+__{>/@}:__ Either '>' or '@' must appear. '>' appears if FASTA files are generated and '@' appears if FASTQ files are generated
+
+__rid:__ Simulated read's index, numbered from 0
+
+__dir:__ The direction of the simulated read. 0 refers to forward strand ('+') and 1 refers to reverse strand ('-')
+
+__sid:__ Represent which transcript this read is simulated from. It ranges between 0 and M, where M is the total number of transcripts. If sid=0, the read is simulated from the background noise. Otherwise, the read is simulated from a transcript with index sid. Transcript sid's transcript name can be found in the 'transcript_id' column of the 'sample_name.isoforms.results' file (at line sid + 1, line 1 is for column names)
+
+__pos:__ The start position of the simulated read in strand dir of transcript sid. It is numbered from 0
+
+__insertL:__ Only appear for paired-end reads. It gives the insert length of the simulated read.
+
+### Example:
+
+Suppose we want to simulate 50 millon single-end reads with quality scores and use the parameters learned from [Example](#example). In addition, we set theta0 as 0.2 and output_name as 'simulated_reads'. The command is:
+
+ rsem-simulate-reads /ref/mouse_125 mmliver_single_quals.stat/mmliver_single_quals.model mmliver_single_quals.isoforms.results 0.2 50000000 simulated_reads