Hi,
I ran flux capacitor on a human BAM file with 9902168 aligned paired end reads (18804336 aligned reads) using the parameter file
ANNOTATION_FILE ensembl_human_71.gtf
COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS]
ANNOTATION_MAPPING PAIRED
Now if I only consider the entries of the output GTF file with feature = "transcript" (ignoring intron and junction entries) and add up the counts-per-million (CPM) values:
RPKM * length / 1000
over all these entries, then I obtain as sum 1568177.63124 although by definition the sum of the CPM values should be 1000000.
Can you comment on this? Why do I get signifcantly more normalized read counts than I should?
Best regrads,
Sven
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