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Title: Software and exemplar data for Rcorrector      
dateReleased:
10-20-2015
privacy:
not applicable
aggregation:
instance of dataset
dateCreated:
10-20-2015
refinement:
curated
ID:
doi:10.5524/100171
creators:
Song, Li
Florea, Liliana
availability:
available
types:
sequence
description:
Next generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, due to the variation in gene expression levels and alternative splicing. We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which employ a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read. The software as published is available directly from here, but for the most up to date version please see the project GitHub https://github.com/mourisl/Rcorrector/ repository.
accessURL: https://doi.org/10.5524/100171
storedIn:
GigaScience Database
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
GigaDB
homePage: http://gigadb.org/
ID:
SCR:006565
name:
Giga Science Database

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