Determining number of reads
 

Hi all,

I am attempting to determine the number of reads associated with each blast hit, and I am wondering if anyone has a resource that could explain how to do this? My goal is to present my data in a way that shows the number of reads from different taxa (e.g., virus families). I know that it might involve mapping back the sequence to my contig (I think?) but usure how I would do this. I am using CLC, and this is from RNA-Seq!