The summarized table of STAR based gene counts (which is then also the basis for STAR based DEseq) contains only strand-unspecific gene counts:
STAR gives a table with 3 different columns: unstranded-counts, strand-specfic-counts, reverse-stranded counts (according to: https://www.biostars.org/p/218995/ I couldn't find that section in the latest manual)
The R function in the pipeline always takes the second column:
readsmatrix[,i] = readspergene[[i]]$V2
It might be a good if its possible to specify whether reads should be strand-specific in the settings file.
borauyar
commented
6 years ago 
The summarized table of STAR based gene counts (which is then also the basis for STAR based DEseq) contains only strand-unspecific gene counts:
STAR gives a table with 3 different columns: unstranded-counts, strand-specfic-counts, reverse-stranded counts (according to: https://www.biostars.org/p/218995/ I couldn't find that section in the latest manual)
The R function in the pipeline always takes the second column: readsmatrix[,i] = readspergene[[i]]$V2
It might be a good if its possible to specify whether reads should be strand-specific in the settings file.