ShortStack input files recommendation

Question

[candron]

Hi All,

I am using ShortStack to identify miRNAs (and other types of sRNAs) from 5 samples of the plant Nicotiana benthamiana - 2 WT and 3 mutants. The samples are fastq files from sRNA sequencing.

Any experience on whether one should run each sample separately with ShortStack or all 5 at the same time? Documentation says that one can specify several readfiles as inputs, but I wonder what's the best strategy here.

Any information would be greatly appreciated.

Thanks in advance!