I'm treating RNA-SEQ with forward-reverse library.

In the doc part 2.5 you explained very well how to configure Strandedness using the python script and the -s reverse option..(as htseqcount...)

In part B of the tutorial,  Preprocessing within R , it's not clear to me how you configure that only using only R with summarizeOverlaps.

I read something GenomicAlignments: Inverting strand when counting using summarizeOverlaps about  preprocess.reads=invertStrand

But that was not clear to me ...

Here I take account of the strand, but finally I'm not sure that it's counting well what it should because I did not succeed to configure library type , could you comment ? Alternative would be to simply set ignore.strand=TRUE to count all reads .

Retrieve 6 Tissue Specific Bam  3 vs 3

bamlst = BamFileList( fls, index=character(), yieldSize=100000, obeyQname=TRUE )

print("SummarizeOverlaps ")
SE = summarizeOverlaps( exonicParts, bamlst, mode="Union", inter.feature=TRUE,singleEnd=FALSE, ignore.strand=FALSE,fragments=FALSE)

colData(SE)$condition =  c("Heart", "Heart", "Heart", "Brain", "Brain", "Brain" ),

data = DDEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon )