pipe.RNAseq | R Documentation |
The top level all-in-one function for turning raw FASTQ files into wiggle tracks, transcriptomes, etc.
pipe.RNAseq( sampleID = NULL, annotationFile = "Annotation.txt", optionsFile = "Options.txt")
pipe.DNAseq( sampleID = NULL, annotationFile = "Annotation.txt", optionsFile = "Options.txt")
pipe.ChIPseq( sampleID = NULL, annotationFile = "Annotation.txt", optionsFile = "Options.txt")
pipe.RIPseq( sampleID = NULL, annotationFile = "Annotation.txt", optionsFile = "Options.txt")
pipeline( sampleID = NULL, annotationFile = "Annotation.txt", optionsFile = "Options.txt")
sampleID |
The SampleID for this sample. This SampleID keys for one row of annotation details in the annotation file, for getting sample-specific details. The SampleID is also used as a sample-specific prefix for all files created during the processing of this sample. |
annotationFile |
File of sample annotation details, which specifies all needed
sample-specific information about the samples under study.
See |
optionsFile |
File of processing options, which specifies all processing
parameters that are not sample specific. See |
Turn raw sequencing reads into final results for that type of data, building various files of results along
the way. pipeline
is a wrapper function that looks at the annotation field DataType
to dispatch
the correct pipeline tool. Main components common to all data types include:
pipe.PreAlignTasks
Setup. Create the results directories (and
cleanup of any previous files) prior to running the pipeline on this sample.
pipe.Alignment
Alignment. Turn FASTQ data into the various types of
alignments via the Bowtie2 alignment program.
pipe.Transcriptome
Transcription (if RNA-seq data) or ChIP Peaks (if ChIP-seq data).
Turn alignments into wiggle tracks, and then generate transcriptome(s) or ChIP peak calls for all target species.
pipe.PostAlignTasks
Optional post-alignment tasks, such as de novo assembly of
No-Hit reads.
For a typical dataset, this top levelpipeline can take many hours to complete, and is usually configured to be run as a batch job submitted to a compute cluster.
a family of data files written to disk, and a text log of all details sent to standard out.
Bob Morrison
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