Extended Data Fig. 9: Multipath alignment benchmark using RNA-seq data from NA12878.

Haplotype-specific transcript (HST) quantification results comparing RPVG with single-path and multipath alignments from VG MPMAP and VG MAP as input using simulated and real Illumina data. For details on the pantranscriptomes used see Supplementary Table 3. The VG MPMAP single-path alignments were created by finding the best scoring path in each multipath alignment. a Recall and precision of whether a transcript is correctly assigned nonzero expression for different expression value thresholds (colored numbers for “Whole (excl. CEU)” pantranscriptome) using simulated data. Expression is measured in transcripts per million (TPM). b Mean absolute relative expression difference (MARD) between simulated and estimated expression (in TPM) for different pantranscriptomes using simulated data. MARD was calculated using either all HSTs in the pantranscriptome (solid bars) or using only the NA12878 HSTs (shaded bars). c Number of expressed transcripts from NA12878 haplotypes shown against the number from non-NA12878 haplotypes for different expression value thresholds (colored numbers) using real data. d Fraction of transcript expression (in TPM) assigned to NA12878 haplotypes for different pantranscriptomes using simulated (left) and real (right) data.