MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.
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ABSTRACT:
SUBMITTER: Cmero M
PROVIDER: S-EPMC8532352 | biostudies-literature | 2021 Oct
REPOSITORIES: biostudies-literature
Publications
MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.
Cmero Marek M Schmidt Breon B Majewski Ian J IJ Ekert Paul G PG Oshlack Alicia A Davidson Nadia M NM
Genome biology 20211022 1
Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting > 85% of v ...[more]
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