HTSeqGenie (version 4.2.0)

HTSeqGenie: Package overview

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)