1. CBBIO
  2. Untitled project
  3. miARma

Source

miARma / Examples / basic_examples / mRNAs / miARma_mRNAs_pipeline.ini

;General parameters
[General]
; type of analysis (miRNA, mRNA or circRNA)
type=mRNA
;0 for no verbose, otherwise to print "almost" everything
verbose=0
; Folder for miRNA reads
read_dir=Examples/basic_examples/mRNAs/reads/
; Number of process to run at the same time
threads=4
; label for the analsysis
label=TSA
; Folder where miARma has been instaled
miARmaPath=.
; Folder to store results
output_dir=Examples/basic_examples/mRNAs/results/
; organism used
organism=human
;Type of sequencing ; could be Paired or Single. [Single by default]
seqtype=Single
#Whether the data is from a strand-specific assay (yes, no or reverse, yes by default) for featureCounts analysis
strand=no

[Quality]
;Character string to put in the name of the results directory
prefix=Pre

[Aligner]
; ; Aligner (Bowtie1, Bowtie2, BWA, miRDeep or Bowtie1-Bowtie2, topHat)
aligner=tophat
; Tophat uses bowtie2 by default, bowtie1 can be also specified. Especifing both, means to repeat the analysis one with each aligner (Allowed values: Bowtie1, Bowtie2 and Bowtie1-Bowtie2/Bowtie2-Bowtie1))
tophat_aligner=Bowtie2
; #Indexed genome to align your reads in format .bt2 (Mandatory for analysis with bowtie2)
bowtie2index=Genomes/Indexes/bowtie2/human/bw2_homo_sapiens19
; ; file used to hold information about gene structure (exos, introns, genes ..)
gtf=Examples/basic_examples/mRNAs/data/Homo_sapiens_GRCh37.74_chr.gtf

[ReadCount]
#GFF file used to calculate the number of reads in featureCounts analysis
database=Examples/basic_examples/mRNAs/data/Homo_sapiens_GRCh37.74_chr.gtf
;GFF attribute to be used as feature ID (default: gene_id) for featureCounts analysis
seqid=transcript_id
; Quality value to avoid counting low quality reads
quality=10
;Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default:exon) for featureCounts analysis
featuretype=exon

[DEAnalysis]
; Complete path of the target file.
targetfile=Examples/basic_examples/mRNAs/data/targets.txt
; Path of the contrast file.
contrastfile=Examples/basic_examples/mRNAs/data/contrast.txt
;This value refers to filter processing in the reads (Should be "yes" or "no").
filter=yes
;Specific software to perform the Differential Expression Analysis (Allowed values: edger, noiseq or edger-noiseq)
desoft=EdgeR-Noiseq
;providing replicates
replicates=yes

[FAnalysis]
; Attribute used (default: gene_id for gene symbol. transcript_id for ensembl transcripts ids, gene_name for gene symbols)
seqid=transcript_id
; #Optional argument to select statistically significant results. 0.8 as default
noiseq_cutoff=0.8
; #Optional argument to select statistically significant results. 0.05 as default
edger_cutoff=0.05

[TargetPrediction]
; #Optional argument to select statistically significant results. 0.8 as default
noiseq_cutoff=0.8
; #Optional argument to select statistically significant results. 0.05 as default
edger_cutoff=0.05
; Use highly diferentually expressed genes
fc_threshold=3