renaming the main mRNA pipeline

Examples/basic_examples/mRNAs/miARma_mRNAs_pipeline_TopHat.ini

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+;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
+;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=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