sc-exon-mapping strand checking

[parsboy66]

Hi Luyi
Thanks for providing sc-pipe.
i have a simple question, whats the meaning of the strand in sc-exon-mapping?? i was trying to use sc-exon-mapping with nanopore data , and i realized that when strnd=T , just few number of the reads can be mapped to exon.
meaning of the strnd=T isnt mapping according to strand??
could you please explain it , why when strnd=F large number of the reads can be mapped to exon but when we use strnd=T number of reads at the output dropped??

Thanks
Iman

[LuyiTian]

some scRNAseq protocols are strand specific, that is why we have this parameter. The nanopore data is generally not strand specific so you should set it to false. if True then the reads need to be mapped to the same strand as the genes.

[parsboy66]

Thanks Luyi👍