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  • BAM alignment and counting

    Hello everyone,
    Can you tell me which is the most common way to quantify the reads from an RNAseq bam file?
    Other that futureCounts, is there anything else well know and reliable?

    Thanks

  • #2
    featureCounts and htseq-count are the most commonly used tools, but you could also use Salmon (with or without alignment) or kallisto (without alignment).

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