Configuration

Configuration

RNAnue can be configured, both, with a configuration file or through the command line, where the latter has precedence. The following table lists the available settings:

General

Parameter	Default	Description
readtype	SE	Read type which can be either single-end (=SE) or paired-end (=PE)
ctrls	-	Absolute path to directory containing the control samples (if available) with additional subdirectories for each library
trtms	-	Absolute path to directory containing the treatment samples with additional subdirectories for each library
outdir	-	Absolute path to directory to store the results of RNAnue
threads	1	Number of threads to use
quality	20	Lower limit of the average quality of the reads to consider in the analysis (Phred Quality Score)
mapquality	20	Lower limit of the average quality of the alignment
minlen	15	Minimum length of the read to consider for the analysis
splicing	0	Whether (=1) or not (=0) splicing events are considered in the detection of split reads

Pre-processing

Parameter	Default	Description
preproc	0	Whether (=1) or not (=0) pre-processing should be performed
modetrm	1	Mode of the read trimming. Only at 5’-end (=0), 3’-end (=1), or both (=2)
adpt5	-	Sequence(s) preceding the 5’-end (N for arbitrary bp) in FASTA format
adpt3	-	Sequence(s) preceding the 3’-end (N for arbitrary bp) in FASTA format
wtrim	-	Whether (=1) or not (=0) to include window trimming in the pre-processing procedure
mmrate	0.1	Allowed mismatch rate in adapter trimming
wsize	3	Window size if window trimming (see wtrim) is enabled
minovlps	5	Minimum overlaps that are required when merging the paired-end reads
dbref	-	Absolute path to FASTA file of the reference
accuracy	90	Minimum percentage of matches per read in read alignment
minfragsco	15	Minimum score of a spliced fragment
minfraglen	15	Minimum length of spliced fragment
minsplicecov	80	Minimum coverage of spliced transcripts
exclclipping	0	Whether (=0) or not (=1) to exclude soft clipping in result

Split Read Calling

Parameter	Default	Description
sitelenratio	0.0	Minimum proportion of the complementarity that covers the read
cmplmin	0.0	Minimum complementarity
nrgmax	0.0	Maximum hybridization energy

Clustering

Parameter	Default	Description
clust	1	Omit (=0) or include (=1) the clustering procedure
clustdist	0	Minimum distance between the clusters

Output

Parameter	Default	Description
stats	1	Produces a statistics file
outcnt	0	Produces a count table in the output
outjgf	0	Produces a JSON graph file of the output