runPipeline: Run the NGS analysis pipeline
In HTSeqGenie: A NGS analysis pipeline.

Description Usage Arguments Details Value Author(s) See Also Examples

Run the NGS analysis pipeline

1	runPipeline(...)

...

A list of parameters. See the vignette for details.

This function starts the pipeline. It first preprocesses the input FASTQ reads, align them, count the read overlaps with genomic features and compute the coverage. See the vignette for details.

The path to the NGS output directory.

Jens Reeder, Gregoire Pau

TP53Genome, TP53GenomicFeatures

## 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)