HTSeqGenie (version 4.2.0)

runPipeline: Run the NGS analysis pipeline

Description

Run the NGS analysis pipeline

Usage

runPipeline(...)

Arguments

...

A list of parameters. See the vignette for details.

Value

The path to the NGS output directory.

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.

See Also

TP53Genome, 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)