+#### a) Converting transcript BAM file into genome BAM file
+
+Normally, RSEM will do this for you via '--output-genome-bam' option
+of 'rsem-calculate-expression'. However, if you have run
+'rsem-prepare-reference' and use 'reference_name.idx.fa' to build
+indices for your aligner, you can use 'rsem-tbam2gbam' to convert your
+transcript coordinate BAM alignments file into a genomic coordinate
+BAM alignments file without the need to run the whole RSEM
+pipeline. Please note that 'rsem-prepare-reference' will convert all
+'N' into 'G' by default for 'reference_name.idx.fa'. If you do not
+want this to happen, please use '--no-ntog' option.
+
+Usage:
+
+ rsem-tbam2gbam reference_name unsorted_transcript_bam_input genome_bam_output
+
+reference_name : The name of reference built by 'rsem-prepare-reference'
+unsorted_transcript_bam_input : This file should satisfy: 1) the alignments of a same read are grouped together, 2) for any paired-end alignment, the two mates should be adjacent to each other, 3) this file should not be sorted by samtools
+genome_bam_output : The output genomic coordinate BAM file's name
+
+#### b) Generating a Wiggle file