I used featureCounts to quantify RNA-seq reads and got a low successful alignment percentage. Is this a problem?

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nf-core nextflow Workflow rna-seq rna

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  • rnaseq

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    • Try https://nf-co.re/rnaseq ! I know it was a lot of work to get to featurecounts, but it actually has been depreciated in favor of either salmon or RSEM quantification. In my experience, STAR-RSEM is the best way to get the most accurate quantification of RNA-Seq data

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