config.yaml

#---------------------------------------------------
#General Parameters 
#---------------------------------------------------
TREAT: "treatment.tsv"
CONTROL: "control.tsv"
TREAT_NAME : "stress" 
CONTROL_NAME : "wildtype"
WORKDIR: '/rds/project/rds-O11U8YqSuCk/SM/RNASeq'
STRAND: 2
N : 2 #Number of replicates
PAIRED: TRUE  #PAIRED is either TRUE or FALSE  
MEMORY: "-Xmx20g" #for 20giga, change as much giga as you have 


#---------------------------------------------------------------
#Choose whether to do genome level or at transcripts level
#---------------------------------------------------------------
LEVEL: GENOME #TRANSCRIPTS #For genome level analysis use GENOME, change to TRANSCRIPTS for transcripts level analysis


#------------------------------------------------------------------
#Change this set of parameters if you wish to run at Genome level 
#------------------------------------------------------------------
GENOME: "/rds/project/rds-O11U8YqSuCk/SM/annotations/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
GTF: "/rds/project/rds-O11U8YqSuCk/SM/annotations/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" 
INDEX: "/rds/project/rds-O11U8YqSuCk/SM/annotations/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/genome"

#-------------------------------------------------------------------------
#Change this set of parameters if you wish to run at transcripts level
#-------------------------------------------------------------------------
TRANSCRIPTS: "/rds/project/rds-O11U8YqSuCk/SM/annotations/Homo_sapiens.GRCh38.cdna.all.fa" 
SALMON_INDEX: "/rds/project/rds-O11U8YqSuCk/SM/annotations/SalmonGRCh38Index" 
SALMON_LIBRARY: SR #strand see Salmon documentation 
TX2GENE: "Ensembltx2gene.txt" 
TXGTF: "/rds/project/rds-O11U8YqSuCk/SM/annotations/Homo_sapiens.GRCh38.104.gtf.gz"