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Fig. 2 | Genome Biology

Fig. 2

From: 2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

Fig. 2

Improved spliced alignment of simulated reads using annotation-guided alignment. a Reference-guided alignment improves the identification of small exons in nanopore DRS reads. Gene track showing the alignment of a sample of simulated nanopore DRS reads at the Arabidopsis FLM gene. AtRTD2 reference annotation, from which reads were simulated, is shown on top, with unguided minimap2 alignments, FLAIR correction of unguided minimap2 alignments, and reference-guided minimap2 alignments shown below. Only reads where exon 6 failed to align in the initial unguided alignment are shown. Each read alignment is colored based on the reference transcript it was simulated from, and reads are shown in the same order within each alignment method group. Mismatches and indels are not shown. b Reference-guided alignment improves the identification of correct transcripts globally. Boxplots with overlaid strip-plots showing the percentage of alignments which map exactly to the splice junctions of the transcript from which they were simulated, for unguided minimap2 alignments, FLAIR correction of unguided minimap2 alignments using reference annotation, and reference annotation-guided minimap2 alignments. Reads simulated from intronless transcripts which map correctly without splicing were not included in percentage calculations. Reads were simulated from Arabidopsis (left) and human (right) nanopore DRS data aligned to the AtRTD2 and GRCh38 reference transcriptomes, respectively

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