I'm hoping someone here can help me. I'm using CLC Workbench's RNA-Seq to map some Illumina data to a reference genome. My question relates to max number of hits: Basically, if you set the max hits to 1 and you have a read that matches to multiple places in the genome (for example an rRNA read) will CLC match to the best read or just throw it out?
Thanks for your help!
Thanks for your help!