منابع مشابه
JAGuaR: Junction Alignments to Genome for RNA-Seq Reads
JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of a single read spanning multiple exons. Reads aligned to the transcript models are then re-mapped on to genomic coordinat...
متن کاملRNASequel: accurate and repeat tolerant realignment of RNA-seq reads
RNA-seq is a key technology for understanding the biology of the cell because of its ability to profile transcriptional and post-transcriptional regulation at single nucleotide resolutions. Compared to DNA sequencing alignment algorithms, RNA-seq alignment algorithms have a diminished ability to accurately detect and map base pair substitutions, gaps, discordant pairs and repetitive regions. Th...
متن کاملGIIRA - RNA-Seq driven gene finding incorporating ambiguous reads
MOTIVATION The reliable identification of genes is a major challenge in genome research, as further analysis depends on the correctness of this initial step. With high-throughput RNA-Seq data reflecting currently expressed genes, a particularly meaningful source of information has become commonly available for gene finding. However, practical application in automated gene identification is stil...
متن کاملCLASS2: accurate and efficient splice variant annotation from RNA-seq reads
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 ...
متن کاملVicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments
Non-coding (nc)RNAs are important structural and regulatory molecules. Accurate determination of the primary sequence and secondary structure of ncRNAs is important for understanding their functions. During cDNA synthesis, RNA 3' end stem-loops can self-prime reverse transcription, creating RNA-cDNA chimeras. We found that chimeric RNA-cDNA fragments can also be detected at 5' end stem-loops, a...
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ژورنال
عنوان ژورنال: Genome Medicine
سال: 2012
ISSN: 1756-994X
DOI: 10.1186/gm403