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Old 07-11-2017, 07:36 AM   #1
Location: Italy

Join Date: Jul 2017
Posts: 34
Default 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?

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Old 07-11-2017, 11:14 PM   #2
Location: Antwerp, Belgium

Join Date: Oct 2015
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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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