HTSeqGenie: Package overview

In HTSeqGenie: A NGS analysis pipeline.

Description

The HTSeqGenie package is a robust and efficient software to analyze high-throughput sequencing experiments in a reproducible manner. It supports the RNA-Seq and Exome-Seq protocols and provides: quality control reporting (using the ShortRead package), detection of adapter contamination, read alignment versus a reference genome (using the gmapR package), counting reads in genomic regions (using the GenomicRanges package), and read-depth coverage computation.

Package content

To run the pipeline:

• runPipeline

To access the pipeline output data:

• getTabDataFromFile

To build the genomic features object:

• buildGenomicFeaturesFromTxDb

• TP53GenomicFeatures

Examples

  ## Not run: 
    ## build genome and genomic features
    tp53Genome <- TP53Genome()
    tp53GenomicFeatures <- TP53GenomicFeatures()
    
    ## get the FASTQ files
    fastq1 <- system.file("extdata/H1993_TP53_subset2500_1.fastq.gz", package="HTSeqGenie")
    fastq2 <- system.file("extdata/H1993_TP53_subset2500_2.fastq.gz", package="HTSeqGenie")
    
    ## run the pipeline
    save_dir <- runPipeline(
        ## input
        input_file=fastq1,
        input_file2=fastq2,
        paired_ends=TRUE,
        quality_encoding="illumina1.8",
        
        ## output
        save_dir="test",
        prepend_str="test",
        overwrite_save_dir="erase",
        
        ## aligner
        path.gsnap_genomes=path(directory(tp53Genome)),
        alignReads.genome=genome(tp53Genome),
        alignReads.additional_parameters="--indel-penalty=1 --novelsplicing=1 --distant-splice-penalty=1",
        
        ## gene model
        path.genomic_features=dirname(tp53GenomicFeatures),
        countGenomicFeatures.gfeatures=basename(tp53GenomicFeatures)
        )
   
## End(Not run)

HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.