I am working with single end RNAseq data and noticed recently that using the different 'library type' (strandedness) options for alignment with Tophat in Galaxy all result in the same alignments. Whether I use 'fr unstranded', 'fr first strand', or 'fr second strand' as the 'library type', the aligned reads for all three settings consistently map to the same strand.
Splice junctions seem to be handled differently (and appropriately) with the different 'library type' options.
I've obtained the same results on Galaxy Main and Galaxy Cloudman.
Insight would be appreciated and I am happy to share an example history.
Thanks in advance!