RNA variant identification discrepancy among splice-aware alignment algorithms
نویسندگان
چکیده
منابع مشابه
Evaluation of tools for long read RNA-seq splice-aware alignment Supplement
For the purpose of the test, error profiles of all real datasets were determined, by aligning them to the corresponding transcriptome using GraphMap (https://github.com/isovic/graphmap) and by running the script errorrates.py from https://github.com/isovic/samscripts. Due to low quality of alignment of ONT Minion RNA reads to the transcriptome, an additional dataset of ONT MinION R9 DNA reads w...
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Next-generation sequencing technologies provide an unparallelled opportunity for the characterization and discovery of known and novel viruses. Because viruses are known to have the highest mutation rates when compared to eukaryotic and bacterial organisms, we assess the extent to which eleven well-known alignment algorithms (BLAST, BLAT, BWA, BWA-SW, BWA-MEM, BFAST, Bowtie2, Novoalign, GSNAP, ...
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RNA-Seq makes it possible not only to measure gene expression but also to identify and quantify transcript isoforms in different experimental conditions. Although a large number of tools allow to infer isoform expression levels from RNA-Seq data, the quantification of alternative splicing variants remains challenging. Aligning reads that span (possibly un-annotated) exon-exon junctions in an ef...
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Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to accurately capture splicing variation has proven difficult. Current programs can find major isoforms of a gene but miss lower abundance variants, or are sensitive but imprecise. CLASS2 is a novel open source tool for ...
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ژورنال
عنوان ژورنال: PLOS ONE
سال: 2018
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0201822