# Online masking uses RepeatMasker as the search engine in the background, # so basically all user parameters of RepeatMasker are retained. We have only made some changes to some parameters. # For example, the optional value of the - lib parameter is changed to dfam / msRepDB, # indicating that the user wants to use dfam library or msRepDB library as the default search library. -s Slow search; 0-5% more sensitive, 2-3 times slower than default -q Quick search; 5-10% less sensitive, 2-5 times faster than default -qq Rush job; about 10% less sensitive, 4->10 times faster than default (quick searches are fine under most circumstances) repeat options -nolow Does not mask low_complexity DNA or simple repeats -noint Only masks low complex/simple repeats (no interspersed repeats) -norna Does not mask small RNA (pseudo) genes -alu Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA) -div [number] Masks only those repeats < x percent diverged from consensus seq -cutoff [number] Sets cutoff score for masking repeats when using -lib (default 225) Contamination options -is_only Only clips E coli insertion elements out of fasta and .qual files -is_clip Clips IS elements before analysis (default: IS only reported) -no_is Skips bacterial insertion element check Running options -gc [number] Use matrices calculated for 'number' percentage background GC level -gccalc RepeatMasker calculates the GC content even for batch files/small seqs -frag [number] Maximum sequence length masked without fragmenting (default 60000) -nocut Skips the steps in which repeats are excised -noisy Prints search engine progress report to screen (defaults to .stderr file) -nopost Do not postprocess the results of the run ( i.e. call ProcessRepeats ). NOTE: This options should only be used when ProcessRepeats will be run manually on the results. output options -a(lignments) Writes alignments in .align output file -inv Alignments are presented in the orientation of the repeat (with option -a) -lcambig Outputs ambiguous DNA transposon fragments using a lower case name. All other repeats are listed in upper case. Ambiguous fragments match multiple repeat elements and can only be called based on flanking repeat information. -small Returns complete .masked sequence in lower case -xsmall Returns repetitive regions in lowercase (rest capitals) rather than masked -x Returns repetitive regions masked with Xs rather than Ns -poly Reports simple repeats that may be polymorphic (in file.poly) -source Includes for each annotation the HSP "evidence". Currently this option is only available with the "-html" output format listed below. -html Creates an additional output file in xhtml format. -ace Creates an additional output file in ACeDB format -gff Creates an additional Gene Feature Finding format output -u Creates an additional annotation file not processed by ProcessRepeats -xm Creates an additional output file in cross_match format (for parsing) -no_id Leaves out final column with unique ID for each element (was default) -e(xcln) Calculates repeat densities (in .tbl) excluding runs of >=20 N/Xs in the query