Differential Expression using Flux capacitor output

Question

[vrehaman]

For Differential expression, we are using tweeDEseq method which will take read counts as input and normalize counts using TMM method and perform pair wise comparisons. As RPKM values already already normalized counts, can I consider "reads" section as raw counts from flux-capacitor output and Is it ok to use the same as input to tweeDEseq?

here is the few lines of output from flux-capacitor

18 ENSEMBL transcript 158483 213739 . + . transcript_id "ENST00000261601.5"; locus_id "18:158483-213739W"; gene_id "ENSG00000101557.8"; **reads 4644.136719**; length 4156; RPKM 2497.995850
18 ENSEMBL transcript 158483 213739 . + . transcript_id "ENST00000383589.1"; locus_id "18:158483-213739W"; gene_id "ENSG00000101557.8"; **reads 2171.213379**; length 4051; RPKM 1198.126099
18 ENSEMBL transcript 158536 211350 . + . transcript_id "ENST00000400266.3"; locus_id "18:158483-213739W"; gene_id "ENSG00000101557.8"; **reads 72.650101**; length 1681; RPKM 96.611931