I have some relatively recent strand specific RNA-seq data which comes as 'second-strand', that means all reads are reversed with respect to the genomic sequence of the transcript and annotation. With featureCounts I would have to use -s 2 option, for example, to get a 70+% rate of assignments to transcripts. But now I am very concerned that the counting went terribly wrong. Does easyRNAseq have an option to set the strand for read assignment, or does it determine those automatically?
I have counted those with the following settings:
bamParam <- BamParam(paired = FALSE, stranded = TRUE, yieldSize = 1000000L) param <- RnaSeqParam(annotParam = annotParam, bamParam = bamParam, countBy = c("transcripts"), precision = "read") ret <- simpleRNASeq(bamFiles = getBamFileList(args), param = param, nnodes = 120, verbose = TRUE, override = TRUE)