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RSeQC | Quality control of RNA-seq experiments

Evaluates different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM/SAM files containing hundreds of millions of alignments.

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RSeQC classification

RSeQC specifications

Unique identifier:
OMICS_01235
Interface:
Command line interface
Input format:
SAM, BAM, BED
Programming languages:
C, Python
Computer skills:
Advanced
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Stability:
Stable

RSeQC distribution

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RSeQC support

Documentation

Credits

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Publications

Institution(s)

Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China

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