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WebSubmitted 11 April 2024 Accepted 20 September 2024 Published 30 October 2024 Corresponding author Xiaoyun He,[email protected] Academic editor Pedro Silva FPKM is very similar to RPKM. RPKM was made for single-end RNA-seq, where every read corresponded to a single fragment that was sequenced. FPKM was made for paired-end RNA-seq. With paired-end RNA-seq, two reads can correspond to a single fragment, or, if one read in the pair did not map, one read can correspond to a single fragment.

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