Additional file 1 of DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing

Additional file 1: Fig. S1. Implementation of hADAR2 editing system in S. pombe. Fig. S2. Confirmation of candidate A-to-I RNA editing sites by sanger sequencing. Fig. S3. Base-calling errors can be used to identify I-type reads in direct Nanopore reads. Fig. S4. Performance of models with different feature selection. Fig. S5. Challenge of reads mapping in repetitive elements by the short-read sequencing. Fig. S6. Changes in potential hydrogen bond interactions between bases induced by A-to-I RNA editing events in transcript NM_002794.5

Additional file 3 of DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing

Additional file 3. Review history

Additional file 2 of DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing

Additional file 2: Table S1. Number of ADAR2-specific errors (ASEs) around editing sites in S.pombe. Table S2. Number of ASEs around random ‘A’ sites in S.pombe. Table S3. Primers used in experiments. Table S4. Predicted editing levels of sites collected from Ramaswami et al. Table S5. Predicted editing levels of sites collected from Peng et al. Table S6. Detected editing sites in Alu regions of 10 human transcripts

Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium-0

<p><b>Copyright information:</b></p><p>Taken from "Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S73-S73.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866708.</p><p></p>ith strong confidence. Light blue regions are D' = 1.0 but decreased confidence. White regions are D' < 1 and state D' within the box. An X denotes that SNP was selected by the program. The gray shading in the HAPLOVIEW row represents the Gabriel blocks. The dark lines represent breaks between blocks for both HAPLOVIEW and HaploBlock Finder. For some chromosomes no blocks were identified and this is indicated by hatch marks across the SNPs