Dealing with multiple-mapped reads in sRNA-seq

Question

[joaquinj12]

I am trying to analyse small RNA-seq data with HtSeq, however, I have read that it is not appropriate enough as it just takes into account uniquely-mapped reads. I have been searching for a user-friendly alternative commonly used to handle with multiple-mapped reads but I have not been able to find one. Will HtSeq-count perform that bad, or do I have to use another tool?

[colindaven]

Try featureCounts -part of subread , you can set the multimapping params as desired