(b) Length distribution of predicted adapters by DeepChopper in VCaP dRNA-seq data.
(c) Distribution of relative adapter position along read length in VCaP dRNA-seq data. Grey rectangle represents a long read from 5′ to 3′. Relative position is calculated as the ratio of the length before DeepChopper predicted adapter start position to the total read length.
(d) Distribution of segments per read after trimming: 1 segment indicates 3′ end adapter trimmed, while 2 or more indicate internal adapters trimmed.
(e) Chimeric alignments (in thousands) for VCaP dRNA-seq reads processed by Dorado with and without adapter trimming, and DeepChopper. DeepChopper greatly reduces chimeric alignments not supported by direct cDNA sequencing.
(f) Distribution of base qualities from identified internal adapters by DeepChopper. Background colors indicate quality levels: green (high), yellow (medium), and red (low).
(g) BLAST-like alignment tool (BLAT) identity distribution of the internal adapter sequences mapping against human reference genome.
(h) The number of chimeric alignments (in thousands) for A549, HCT116, HepG2, K562, and MCF7 cell lines processed by Dorado with adapter trimming and DeepChopper. DeepChopper consistently reduces chimeric alignments not supported by cDNA sequencing across all cell lines.
(i) Chimeric alignments from dRNA-seq of the WTC11 cell line, evaluated for support using additional ONT and Pacific Biosciences (PacBio) sequencing data with different protocols. DeepChopper reduces unsupported chimeric alignments across all methods compared to Dorado with adapter trimming.