REDItoolDenovo.py has been conceived to predict potential RNA editing events using RNA-Seq data alone and without any a priori knowledge about genome information and biological properties of RNA editing phenomenon.
REDItoolDenovo.py -i rnaseq.bam -f reference.fa
-i BAM file
-I Sort input BAM file
-f Reference in fasta file
-k List of chromosomes to skip separated by comma or file
-t Number of threads 
-o Output folder [rediFolder_XXXX] in which all results will be stored. XXXX is a random number generated at each run.
-F Internal folder name [null] is the main folder containing output tables.
-b Use input distribution file
-a Fisher Tail [l, r, t] [default l] [l=left_tail, r=right_tail, t=two_tail]
-c Min. read coverage 
-Q Fastq offset value 
-q Min. quality score 
-m Min. mapping quality score 
-O Min. homoplymeric length 
-s Infer strand (for strand oriented reads) . It indicates which read is in line with RNA. Available values are: 1:read1 as RNA,read2 not as RNA; 2:read1 not as RNA,read2 as RNA; 12:read1 as RNA,read2 as RNA; 0:read1 not as RNA,read2 not as RNA.
-g Strand inference type 1:maxValue 2:useConfidence ; maxValue: the most prominent strand count will be used; useConfidence: strand is assigned if over a prefixed frequency confidence (-x option)
-x Strand confidence [0.70]
-S Strand correction. Once the strand has been inferred, only bases according to this strand will be selected.
-G Infer strand by gff annotation (must be sorted, otherwise use -X)
-X Sort annotation files
-K File with positions to exclude
-e Exclude multi hits
-d Exclude duplicates
-l Select significant sites
-V Significant value [0.05]
-w Statistical test [BH, BO, NO] [default BH] [BH=Benjamini, BO=Bonferroni, NO=No Correction]
-U Use specific substitutions separated by comma [example: AG,TC]
-p Use paired concardant reads only
-u Consider mapping quality
-T Trim x bases up and y bases down per read [0-0]
-B Blat folder for correction
-W Remove substitutions in homopolymeric regions
-v Minimum number of reads supporting the variation 
-n Minimum editing frequency [0.1]
-E Exclude positions with multiple changes
-P File containing splice sites annotations (SpliceSite file format see above for details)
-r Number of bases near splice sites to explore 
-h Print the help