pipe.AlignStats | R Documentation |
Auxiliary pipeline step that creates a family of alignment statistic images to summarize all aspects of the alignment pipeline and its metrix.
pipe.AlignStats( sampleID, annotationFile = "Annotation.txt", optionsFile = "Options.txt",
results.path = NULL, banner = "", chunkSize = 500000, maxReads = NULL,
mode = c( "normal", "QuickQC"), what = NULL, plot = TRUE, fastqFile = NULL)
pipe.AlignmentPie( sampleID, annotationFile = "Annotation.txt", optionsFile = "Options.txt",
results.path = NULL, banner = "", mode = c( "normal", "QuickQC"),
fastqFile = NULL, useUSR = TRUE)
sampleID |
The SampleID for 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 |
results.path |
The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'. |
banner |
Optional character string to add to each plot's main heading. |
chunkSize |
Integer. The buffer size to use for reading in and evaluating alignments. Most statistics are tallied and images printed after each buffer, to show incremental progress. |
maxReads |
Optional integer to limit the number of alignments evaluated. |
mode |
Controls the behavior of how alignments are interpreted. Mode |
what |
An optional character string that specifies which types of statistics to monitor. Default is to monitor every type of feature, or "SGBIDMA" where: S: Sequences: features about chromosome, like read counts and percentages. G: Genes: features about genes, like read counts and percentages for highly detected genes. B: Bases: features about base calls, locations of mismatches, and nucleotide usage. I,D: Insertions & Deletions: features about indel locations in the aligned reads. M: MARs (Multiply Aligned Reads): features about reads hitting 2+ locations. A: Align scores: features about the distribution of Bowtie alignment scores. |
fastqFile |
Optional character string for the original FASTQ file that was input to the alignment pipeline. Default is to look it up from annotation file. |
useUSR |
Logical. Include a survey of USRs (Unique Short Reads) in the pie, to assess presence of empty adapters, Poly-N, etc. |
This pipeline step tries to evaluate every aspect of how well the raw reads aligned to the target organism(s). It generates a large family of plot images, each of which shows some measure of alignment success or failure.
A family of files and plot images is created on disk under the subfolder AlignStats
.
Also a list of read counts and percentages as returned from the alignment pie function that summarizes the alignment status of the entire sample.
Bob Morrison
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