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  • mapping software

    Hi

    Does anyone know if there is a mapping/short read aligner software that gives me the information of how many total alignments this read has?

    i.e. I want to map to the genome RNA-seq reads, get as output only 1 alignment for each read, but also get the information of how many other alignments this read has - only the number of alignments without the full chr+position.


    Thanks.

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