REDItoolKnown.py has been developed to explore the RNA editing potential of RNA-Seq data sets using known editing events. Such events can be downloaded from DARNED database or generated from supplementary materials of a variety of publications. Known RNA editing events have to be stored in TAB files (see above for details).
REDItoolKnown.py -i rnaseq.bam -f reference.fa -l knownEditingSites.tab
Options:
-i BAM file
-I Sort input BAM file
-f Reference in fasta file
-l List of known RNA editing events
-C Base interval to explore [100000]
-k List of chromosomes to skip separated by comma or file
-t Number of threads [1]
-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.
-c Min. read coverage [10]
-Q Fastq offset value [33]
-q Minimum quality score [25]
-m Minimum mapping quality score [25]
-O Minimum homoplymeric length [5]
-s Infer strand (for strand oriented reads) [1]. 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 [1]; 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). Sorting requires grep and sort unix executables.
-X Sort annotation files. It requires grep and sort unix executables.
-K File with positions to exclude (chromosome_name coordinate)
-e Exclude multi hits
-d Exclude duplicates
-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
-U Remove substitutions in homopolymeric regions
-v Minimum number of reads supporting the variation [3]
-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 Num. of bases near splice sites to explore [4]
-h Print the help