Dealing with multiple-mapped reads in sRNA-seq
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?
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joaquinj12 •
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Try featureCounts -part of subread , you can set the multimapping params as desired