Fig 1.
An overview of iMapSplice algorithm.
(A) An example illustrating the challenge when mapping a RNA-seq read to the reference genome in the presence of SNPs. (B) An example illustrating how iMapSplice algorithm may resolve spliced alignment with SNPs as well as the basic steps of the alignment.
Table 1.
The set of tools and their index configuration used in performance comparison.
Table 2.
The comparison of five baseline tools in terms of the number of accurate unique alignments out of 20 million synthetic reads in each of the four datasets with different read lengths and error profiles.
Fig 2.
Aggregated reference allelic ratio distribution of different methods on RNA-seq datasets from individuals NA12812, NA12749, NA07056, NA06994, and NA12275.
(A) Comparison between iMapSplice-phased and “Ref-based” methods (MapSplice, HISAT2, and STAR); (B) Comparison between iMapSplice-phased and “Mask-based” methods (MapSplice MASK, HISAT2 MASK, and STAR MASK); (C) Comparison between two variants of iMapSplice and “SNP-aware” methods (HISAT2 SNP and HISAT2 POP); (D) Summarized comparison in terms of mean and skewness for reference allelic ratio distributions, and number of SNPs covered by at least ten reads.
Table 3.
Detected personal splice junctions changing from noncanonical to canonical with increasing numbers of supporting individuals and reads.
Table 4.
Number of splice junctions falling into each category of average coverage changes between the individuals of with and without polymorphisms in splice sites.
The polymorphisms changed the splice sites from noncanonical to canonical.
Table 5.
Number of splice junctions falling into each category of average coverage changes between the individuals with and without polymorphisms in splice sites.
The polymorphisms changed the splice sites from canonical to noncanonical.
Fig 3.
Examples of splice site polymorphisms.
The solid lines with numbers indicate splice junctions with a polymorphism in the donor or acceptor site, while the dashed lines with numbers indicate other “normal” splice junctions that share either the donor or acceptor sites with the polymorphic splice junctions, but have no polymorphisms. The vertical solid red lines indicate the splice sites where the polymorphism converts a noncanonical splice site to a canonical site, while the vertical solid blue lines indicate the splice sites where the polymorphism converts a canonical splice site to a noncanonical splice site. The vertical dashed gray lines indicate the unshared splice sites of “normal” splice junctions. Bases in black are the reference nucleotides, while those in red are alternate bases at SNP positions. The numbers along the splice junctions are the supporting read counts in the specific RNA-seq sample. The five RNA-seq samples used to demonstrate the examples are from individuals NA12812, NA12749, NA07056, NA12275, and NA06994. (A) and (B) are examples of splice site polymorphisms that enhance splicing through the creation of canonical splice site dinucleotide; (C) is the example of splice site polymorphism that disables splicing as a result of the loss of canonical splice site dinucleotide.
Table 6.
Indexing file size and running time to align the 74 RNA-seq dataset reads.
Note: indexing file storage usage and run time for HISAT2 SNP and rPGA are estimated according to their performance on five randomly selected datasets.