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1. We scan through each of the BAM files and find all the transcripts that have meet the minimum coverage threshold.
2. With those transcripts, we "create" an annotation file that has the transcript name as the sequence name and the Gene ID and the Transcript ID have the same transcript name. The start position is 1 and the end position is the length of the transcript. 
3. Effectively, what the annotation file does is filter out the low coverage transcripts.
4. Since we don't know where the transcripts are in the genome, chromosome view will display only one transcript at a time (i.e., the transcript names are treated like "chromosomes").

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