A direct comparison of genome alignment and transcriptome pseudoalignment

Abstract

Motivation: Genome alignment of reads is the first step of most genome analysis workflows. In the case of RNA-Seq, transcriptome pseudoalignment of reads is a fast alternative to genome alignment, but the different coordinate systems of the genome and transcriptome have made it difficult to perform direct comparisons between the approaches. Results: We have developed tools for converting genome alignments to transcriptome pseudoalignments, and conversely, for projecting transcriptome pseudoalignments to genome alignments. Using these tools, we performed a direct comparison of genome alignment with transcriptome pseudoalignment. We find that both approaches produce similar quantifications. This means that for many applications genome alignment and transcriptome pseudoalignment are interchangeable. Availability and Implementation: bam2tcc is a C++14 software for converting alignments in SAM/BAM format to transcript compatibility counts (TCCs) and is available at https://github.com/pachterlab/bam2tcc. kallisto genomebam is a user option of kallisto that outputs a sorted BAM file in genome coordinates as part of transcriptome pseudoalignment. The feature has been released with kallisto v0.44.0, and is available at https://pachterlab.github.io/kallisto/.