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A direct comparison of genome alignment and transcriptome pseudoalignment

Yi, Lynn and Liu, Lauren and Melsted, Páll and Pachter, Lior (2018) A direct comparison of genome alignment and transcriptome pseudoalignment. . (Unpublished)

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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 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

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Yi, Lynn0000-0003-4575-0158
Melsted, Páll0000-0002-8418-6724
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. bioRxiv preprint first posted online Oct. 16, 2018. Availability and Implementation: bam2tcc is available at kallisto v0.44.0 containing the novel genomebam feature is available at The scripts and code used to regenerate our analysis are available at We thank Valentine Svensson for helpful feedback during the implementation of bam2tcc. Funding: LY was funded by the UCLA/Caltech MSTP, NIH T32 GM007616, NIH U19MH114830, the Lee Ramo Endowment, the Treadway Endowment, and the Hearst Endowment. LP was partly funded by U19MH114830.
Funding AgencyGrant Number
UCLA-Caltech Medical Scientist Training ProgramUNSPECIFIED
NIH Predoctoral FellowshipT32 GM007616
Lee Ramo EndowmentUNSPECIFIED
Treadway EndowmentUNSPECIFIED
Hearst EndowmentUNSPECIFIED
Record Number:CaltechAUTHORS:20181029-160959571
Persistent URL:
Official Citation:A direct comparison of genome alignment and transcriptome pseudoalignment. Lynn Yi, Lauren Liu, Pall Melsted, Lior Pachter. bioRxiv 444620; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90482
Deposited By: Tony Diaz
Deposited On:30 Oct 2018 01:50
Last Modified:16 Nov 2021 03:33

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