params.cfg

### GENERAL
readtype = SE # paired-end (PE) or single-end (SE)

# absolute path of dirs containing the raw reads (additional dir for each library)
trtms = /Users/riasc/Documents/work/projects/RNAnue/rawreads_100k/trtms/ # treatments 
ctrls = /Users/riasc/Documents/work/projects/RNAnue/rawreads_100k/ctrls/ # controls 
outdir = /Users/riasc/Documents/work/projects/RNAnue/results_100k/ # dir 

threads = 4 # number of threads 
quality = 20 # lower limit for the average quality (Phred Quality Score) of the reads
mapquality = 20 # lower limit for the average quality (Phred Quality Score) of the alignment
minlen = 20 # minimum length of the reads
splicing = 0 # include splicing (=1) or not (=0)

### DATA PREPROCESSING 
preproc = 1 # preprocessing of the reads can be either omitted (=0) or included (=1) 
modetrm = 1 # mode of the trimming: only 5' (=0) and 3' (=1) or both (=2) 
# sequence preceeding 5'-end (N for arbitrary bp) in .fa format
adpt5 =  
# sequence succeeding 3'-end (N for arbitrary bp) in fa. format
adpt3 = /Users/riasc/Documents/work/projects/RNAnue/build/adapters3.fa 
wtrim = 0 # on whether (=1) or not (=0) to include window quality trimming
# rate of mismatches allowed when aligning adapters with read sequence 
mmrate = 0.1 # e.g., 0.1 on a sequence length of 10 results in
wsize = 3 # window size 
minovlps = 5 # minimum overlaps required when merging paired-end reads

### ALIGNMENT (forwarded to segemehl.x)
dbref = /Users/riasc/Documents/work/projects/RNAnue/build/ecoli_bl21_de3.fasta
accuracy = 90 # min percentage of matches per read in semi-global alignment
minfragsco = 15 # min score of a spliced fragment 
minfraglen = 15 # min length of a spliced fragment
minsplicecov = 80 # min coverage for spliced transcripts
mapq = 20 # min mapping quality for spliced transcripts
exclclipping = 0 # exclude soft clipping from
unprd = 0 # only for paired-end reads: include unpaired reads in the subsequent analysis
unmrg = 0 # only for paired-end reads: include unmerged reads in the subsequent analysis

### SPLIT READ CALLING 
sitelenratio = 0.0
cmplmin = 0.0 # complementarity cutoff - consider only split reads that exceed cmplmin
nrgmax = 0 # hybridization energy cutoff - consider only split reads that fall beneath nrgmax

### CLUSTERING
clust = 1 # clustering of the split reads can either be omitted (=0) or included (=1)
clustdist = 0 # minimum distance between clusters

### ANALYIS
# specify the annotations of the organism of interest (optional)
features = /Users/riasc/Documents/work/projects/RNAnue/build/ecoli_BL21_DE3.gff # GFF3 feature file

# OUTPUT
stats = 1 # produce a statistics of the libraries
outcnt = 1 # (additionally) produce a count table as output
outjgf = 1 # (additionally) produce a JSON graph file for visualization