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(A) Two similar reference transcripts with similar mapping. (B) Using fast5_fetcher to extract raw files. (C) SquigglePull and SquigglePlot converting to.tsv and plotting the signal. (D) Adapter stalls and poly-A tail identified using Segmenter. (E) Converting last 20 nt of the 3’ end to a signal using a pore current model and aligning this synthetic signal to the empirical signal (dashed grey lines) by backtracking through a dynamic programming matrix (white trace)
