DuffyNGS_Annotation: Annotation File of Sample-Specific Settings

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Annotation File of Sample-Specific Settings

Description

The Annotation file defines the SampleID and several sample-specific settings for each dataset to be processed. See DuffyNGS_Options for processing settings that are not specific to each sample. Each column is a named field, and all entries are tab-delimited. See AnnotationTable for more details.

Annotation Fields

SampleID

The SampleID for this sample. This SampleID keys for one entire 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.

Filename

File(s) of raw read data to be aligned; most commonly FASTQ format. In the case of paired end data, this field will be 2 filenames, separated by a comma with no intervening spaces.

PairedEnd

Logical. Is this sample a paired end dataset, with 2 separate files of raw reads.

DataType

A data type for this sample. One of: RNA-seq, DNA-seq, ChIP-seq, RIP-seq

Group

A GroupID for this sample, for processing tools that combine samples by various traits. Most such tools allow you to specify the grouping field by a groupColumn argument.

Color

A color for this sample, for processing tools that visualize multiple samples. Most such tools allow you to specify the color field by a colorColumn argument.

ReadSense

The read orientation for this sample. One of: sense, antisense This can depend on the details of sample prep, library construction, and sequencer. It is used if you expect to have strand specific reads, and controls which strand the reads get assigned to.

StrandSpecific

Logical. Did the details of sample prep, library construction, and sequencing generate strand specific reads, and should reads only count toward expression totals, etc., if they land on the correct (coding) strand.

KeepIntergenics

Logical. Should extra 'non-genes' be explicitly added to capture expression, etc., in the intergenic spaces. This field is queried by each tool, so it may be necessary to re-run some steps. (e.g. differential expression is based on transcription, so adding non-genes to the DE results requires that the transcription tool was run with KeepIntergenics = TRUE

ExonsOnly

Logical. Should the entire extent of the gene's location on the chromosome be used when RPKM values are calculated, or should the tool restrict to only use regions inside the defined exons.

TargetID

an optional character string to define the TargetID for this sample. If present, overrides the default in the options table. This is useful when there are multiple mixed organisms within one experiment.

Note

The annotation file can contain any other columns as well. Typically it may have more than one column of grouping and coloring information, as samples may be compared in multiple ways. Most sample comparison tools have explicit groupColumn and colorColumn arguments to easily identify how samples will be grouped and colored.

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.