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I ran flux capacitor on a human BAM file with 9902168 aligned paired end reads (18804336 19804336 aligned reads ) using the which equals the number of SAM records as I consider primary alignments only); I used the parameter file

  ANNOTATION_FILE ensembl_human_71.gtf

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Can you comment on this? Why do I get signifcantly more normalized read counts than I should?

One way to deal with this is to renormalize the data so that the CPM add up to 1000000. Another question would be whether this renormalization also need to be applied to intron and junction counts.

Best regrads,

Sven