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?
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
Overview
Content Tools