####README ####This is the configuration file for running the RNA Editing Site Analysis (REA) module of CPGAVAS2 web server ####Last modified: April 12, 2019 ####lines started with "#" are comments and will be ignored ####The format of the file are: #### tophat:: #### or #### reditools:: ####Some parameters do not have value. #####DEFAULT SETUP tophat:--library-type:fr-firststrand tophat:--read-edit-dist:7 reditools:-s:12 reditools:-c:5 reditools:-l reditools:-t:7 reditools:-v:1 #####DEFAULT SETUP #####Below are the list of parameters you can set and the meaning of them ########tophat2 paramerters, all of them should be prefixed with tophat: #Usage: # tophat [options] [reads1[,reads2,...]] \ # [quals1,[quals2,...]] [quals1[,quals2,...]] #Options: # -v/--version # -o/--output-dir [ default: ./tophat_out ] # --bowtie1 [ default: bowtie2 ] # -N/--read-mismatches [ default: 2 ] # --read-gap-length [ default: 2 ] # --read-edit-dist [ default: 2 ] # --read-realign-edit-dist [ default: "read-edit-dist" + 1 ] # -a/--min-anchor [ default: 8 ] # -m/--splice-mismatches <0-2> [ default: 0 ] # -i/--min-intron-length [ default: 50 ] # -I/--max-intron-length [ default: 500000 ] # -g/--max-multihits [ default: 20 ] # --suppress-hits # -x/--transcriptome-max-hits [ default: 60 ] # -M/--prefilter-multihits ( for -G/--GTF option, enable # an initial bowtie search # against the genome ) # --max-insertion-length [ default: 3 ] # --max-deletion-length [ default: 3 ] # --solexa-quals # --solexa1.3-quals (same as phred64-quals) # --phred64-quals (same as solexa1.3-quals) # -Q/--quals # --integer-quals # -C/--color (Solid - color space) # --color-out # --library-type (fr-unstranded, fr-firststrand, # fr-secondstrand) # -p/--num-threads [ default: 1 ] # -R/--resume ( try to resume execution ) # -G/--GTF (GTF/GFF with known transcripts) # --transcriptome-index (transcriptome bowtie index) # -T/--transcriptome-only (map only to the transcriptome) # -j/--raw-juncs # --insertions # --deletions # -r/--mate-inner-dist [ default: 50 ] # --mate-std-dev [ default: 20 ] # --no-novel-juncs # --no-novel-indels # --no-gtf-juncs # --no-coverage-search # --coverage-search # --microexon-search # --keep-tmp # --tmp-dir [ default: /tmp ] # -z/--zpacker [ default: gzip ] # -X/--unmapped-fifo [use mkfifo to compress more temporary # files for color space reads] # #Advanced Options: # --report-secondary-alignments # --no-discordant # --no-mixed # # --segment-mismatches [ default: 2 ] # --segment-length [ default: 25 ] # # --bowtie-n [ default: bowtie -v ] # --min-coverage-intron [ default: 50 ] # --max-coverage-intron [ default: 20000 ] # --min-segment-intron [ default: 50 ] # --max-segment-intron [ default: 500000 ] # --no-sort-bam (Output BAM is not coordinate-sorted) # --no-convert-bam (Do not output bam format. # Output is /accepted_hits.sam) # --keep-fasta-order # --allow-partial-mapping # #Bowtie2 related options: # Preset options in --end-to-end mode (local alignment is not used in TopHat2) # --b2-very-fast # --b2-fast # --b2-sensitive # --b2-very-sensitive # # Alignment options # --b2-N [ default: 0 ] # --b2-L [ default: 20 ] # --b2-i [ default: S,1,1.25 ] # --b2-n-ceil [ default: L,0,0.15 ] # --b2-gbar [ default: 4 ] # # Scoring options # --b2-mp , [ default: 6,2 ] # --b2-np [ default: 1 ] # --b2-rdg , [ default: 5,3 ] # --b2-rfg , [ default: 5,3 ] # --b2-score-min [ default: L,-0.6,-0.6 ] # # Effort options # --b2-D [ default: 15 ] # --b2-R [ default: 2 ] # #Fusion related options: # --fusion-search # --fusion-anchor-length [ default: 20 ] # --fusion-min-dist [ default: 10000000 ] # --fusion-read-mismatches [ default: 2 ] # --fusion-multireads [ default: 2 ] # --fusion-multipairs [ default: 2 ] # --fusion-ignore-chromosomes [ e.g, ] # # --fusion-do-not-resolve-conflicts [this is for test purposes ] # #SAM Header Options (for embedding sequencing run metadata in output): # --rg-id (read group ID) # --rg-sample (sample ID) # --rg-library (library ID) # --rg-description (descriptive string, no tabs allowed) # --rg-platform-unit (e.g Illumina lane ID) # --rg-center (sequencing center name) # --rg-date (ISO 8601 date of the sequencing run) # --rg-platform (Sequencing platform descriptor) # # for detailed help see http://ccb.jhu.edu/software/tophat/manual.shtml # ###### ###### ######reditools parameters, all of them should be prefixed with "reditools" # Options: # -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 [1] # -F Internal folder name [null] # -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 [10] # -Q Fastq offset value [33] # -q Min. quality score [25] # -m Min. mapping quality score [20] # -O Min. homoplymeric length [5] # -s Infer strand (for strand oriented reads) [1] # -g Strand inference type 1:maxValue 2:useConfidence [1] # -x Strand confidence [0.70] # -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 Min. num. of reads supporting the variation [3] # -n Min. editing frequency [0.1] # -E Exclude positions with multiple changes # -P File containing splice sites annotations # -r Num. of bases near splice sites to explore [4] # -h Print this help