rseqc

Version:
4.0.0
Identifier: TL_73aadb.49
Tool

Description


Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.

Subtools

  • rseqc read_distribution

    The tool calculates the fraction of reads mapped to coding exons, 5'-UTR exons, 3'-UTR exons, introns and intergenic regions based on the gene models

  • rseqc read_quality

    make read quality histogram

  • rseqc junction_saturation

    check if current sequencing depth is deep enough to perform alternative splicing analyses

  • rseqc infer_experiment

    This program is used to guess how RNA-seq sequencing were configured, particulary how reads were stranded for strand-specific RNA-seq data, through co

  • rseqc bam_stat

    This tool can be used to check the mapping statistics of reads - number of uniquely mapped reads, number reads mapped over a splice junction, number o

  • rseqc junction_annotation

    For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED format, this program will compare detected splice junction

  • rseqc FPKM_count

    Calculate raw read count, FPM (fragment per million) and FPKM (fragment per million mapped reads per kilobase exon) for each gene in BED file. Note SA

  • rseqc geneBody_coverage

    This tool scales all transcripts to 100nt and calculates the number of reads covering each nucleotide position.