;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=reads/mRNA_reads/
; label for the analsysis
label=mRNA_cancer_colon
; ; Folder where miARma has been instaled
miARmaPath=.
; Number of process to run at the same time
threads=16
; Folder to store results
output_dir=miARma_mRNA_results/
; organism used
organism=human
;Type of sequencing ; could be Paired or Single. [Single by default]
seqtype=Paired
#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, Hisat2, star)
aligner=Hisat2
; #Indexed genome to align your reads in format .bt2 (Mandatory for analysis with bowtie2)
hisat2index=Genomes/Indexes/hisat2/human/his_homo_sapiens19

[ReadCount]
#GFF file used to calculate the number of reads in featureCounts analysis
database=../../data/gencode.v26_GRCh37.annotation.gtf
;GFF attribute to be used as feature ID (default: gene_id) for featureCounts analysis
seqid=gene_name
; Quality value to avoid counting low quality reads
quality=25
;Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default:exon) for featureCounts analysis
featuretype=exon
;adding paratemter to include multimapping reads
parameters=-C -B -M -O

[DEAnalysis]
; Complete path of the target file.
targetfile=data/mRNA_targets.txt
; Path of the contrast file.
contrastfile=data/mRNA_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
;providing replicates
replicates=yes
;Provide a file with normalized reads
cpm=yes
;Provide a file with RPKM values
rpkm=yes

[FAnalysis]
; Attribute used (default: gene_id for gene symbol. transcript_id for ensembl transcripts ids, gene_name for gene symbols)
seqid=gene_name