RSeQC is a package that contains multiple tools that can be implemented for quality control of high throughput sequencing data, including functions for sequence quality, nucleotide composition, GC and PCR bias, sequencing depth, strand specificity, mapped reads distribution, coverage uniformity, RNA integrity, and genomic read distribution. RSeQC takes both SAM and BAM files as input.

References:

Liguo Wang, Shengqin Wang, Wei Li, RSeQC: quality control of RNA-seq experiments, Bioinformatics, Volume 28, Issue 16, 15 August 2012, Pages 2184–2185, https://doi.org/10.1093/bioinformatics/bts356

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