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Fig. 5 | BMC Genomics

Fig. 5

From: Indel detection from DNA and RNA sequencing data with transIndel

Fig. 5

Indel detection on RNA-seq data. a transIndel workflow of calling indels from RNA-seq data. b The composition of functionally important regions for detected indels within annotated genes in WES and RNA-seq data from AACR-PCF-SU2C samples. c Comparison of the indel variant allele fractions derived from RNA-seq and WES data from AACR-PCF-SU2C samples. The line shows a fitted linear regression model with 95% confidence interval. d Overlap in coding indels detected from WES and RNA-seq data from AACR-PCF-SU2C samples. Over half of the indels detected in WES data were not detected in RNA-seq data because of no RNA expression, or RNA expression from the un-affected, reference allele. e Candidate recurrent exitron splicing events in tumor suppressor genes (TGS) and other cancer-related genes in metastatic castration-resistant prostate cancer. f Validation of a 112 bp ZBTB18 exitron splicing event in RNA but not DNA from the LNCaP cell line. Genomic coordinates are hg19. RT = reverse transcriptase, NRT = no reverse transcriptase. Reverse transcription reactions were primed with oligo-dT primers or random hexamers as indicated

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