ArticleBMC bioinformatics2015
ContextMap 2: fast and accurate context-based RNA-seq mapping.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes.Nature communications · 2023Article
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- HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes.Journal of virology · 2023Article
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- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity.Science advances · 2021Article
- Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics.Communications biology · 2021Article
- Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level.Journal of virology · 2021Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMapping of short sequencing reads is a crucial step in the analysis of RNA sequencing (RNA-seq) data. ContextMap is an RNA-seq mapping algorithm that uses a context-based approach to identify the best alignment for each read and allows parallel mapping against several reference genomes.
resultsIn this article, we present ContextMap 2, a new and improved version of ContextMap. Its key novel features are: (i) a plug-in structure that allows easily integrating novel short read alignment programs with improved accuracy and runtime; (ii) context-based identification of insertions and deletions (indels); (iii) mapping of reads spanning an arbitrary number of exons and indels. ContextMap 2 using Bowtie, Bowtie 2 or BWA was evaluated on both simulated and real-life data from the recently published RGASP study.
conclusionsWe show that ContextMap 2 generally combines similar or higher recall compared to other state-of-the-art approaches with significantly higher precision in read placement and junction and indel prediction. Furthermore, runtime was significantly lower than for the best competing approaches. ContextMap 2 is freely available at http://www.bio.ifi.lmu.de/ContextMap .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.