DuffyNGS_Options: Options File of Processing Settings

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

Options File of Processing Settings

Description

The Options file defines the various processing settings for all datasets to be processed. See DuffyNGS_Annotation for settings that are specific to each sample. There are 2 columns OptionName, Value and all entries are tab-delimited. See OptionsTable for more information.

Details

The motivation behind the Options file is to allow the end user a large degree of control over the run time behavior of the DuffyNGS pipeline. A fixed set of parameters and command arguments can be altered by changing the entries in this file. If there are addititional fields that you want finer control over, contact the authors.

Options

targetID

The TargetID for processing the samples. This specifies the set of species that the raw data will be aligned against, etc. See Targets. Default is HsPf

nCores

Enables parallel execution using multiple cores. Sets the maximum number of cores to use simultaneously. Most low level functions that operate on chromosomes are written to do chromosomes in parallel. See multicore.setup.

genomicFastaFile

Full pathname to the file (or folder) of genomic DNA for this set of species. In the case of very large genomes, it can be the folder name that contains FASTA files for each chromosome.

fastqData.path

Full pathname of the folder that contains the raw read datasets to be aligned. This will be combined with the actual filename from the Annotation file to build the complete pathname for a sample's raw FASTQ files.

results.path

Full pathname of the folder that will receive all generated results files for all processed samples. It will be created if it does not yet exist. Default is "."

tmp.path

Explicit full pathname to temporary storage on the current compute node. Used for temporary large scratch disk space.

bowtie2Program

Full pathname of the Bowtie2 executable to be used for alignments.

bowtie2Index.path

Full pathname to the folder of Bowtie2 alignment indexes. The final filename for an index will be constructed from this path and the named index for each alignment step. See below.

bowtie2InputOptions

A character string of Bowtie parameters affecting how the raw reads are interpreted. This includes hard trimming, fastq format, quality score type, etc.

bowtie2PairOptions

A character string of Bowtie parameters affecting paired end behavior.

trim5

trim3

Integer. Hard trimming of bases. These will be passed to Bowtie2, and are used by other DuffyNGS tools that need to treat the raw reads exactly as Bowtie did.

maxMultiHits

Integer. Controls the maximum number of chromosomal locations reported by Bowtie for an aligned read. Passed to Bowtie as its '-k' options.

readBufferSize

Integer. Controls memory usage for pipeline steps that operate on reads in a buffered manner. Larger size will run faster but consume more memory.

DE.minimumRPKM

Numeric. Used to prevent dividing by very low or zero expression values. Added as an offset to most ratio and fold change calculations. Sensible values vary by the size of the genome. If set too high then true fold change will be under reported. If set too low, then unexpressed genes may be reported as having extremely large fold change.

DE.weightFoldChange

DE.weightPvalue

Numeric weights that set the relative importance of these two primary metrics for ordering differentially expressed genes. See diffExpressRankOrder.

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