Exon_reads.gct.gz file raw count data are not integer

[zhangpicb]

Dear @agraubert @joshua-gould @francois-a @dmcgoldrick

Thanks for the great tool!

I have a simple question.Why exon_reads.gct.gz file raw count data are not integer?gene_reads.gct.gz files raw count data are integer?

Thanks in advanced!

[agraubert]

The exon reads file counts partial reads (length of intersection with an exon / length of the read)

[zhangpicb]

The exon reads file counts value is sum(length of intersection with the exon )/sum(full length of the read overlap the exon) ?

[agraubert]

sum([length of intersection / read length], [length of intersection / read length] ....)

rnaseqc/src/Expression.cpp

Lines 345 to 346 in 6465cb4

	double tmp = static_cast<double>(intersectionSize) / length;
	exonCoverageCollector.add(result->gene_id, result->feature_id, tmp);

[zhangpicb]

Thanks a ton!