Rlooper with additional feature: ssDNA nicking and simulate peaks from a given DNA
rlooper_sim --i <fastaFile.fa> --outdir <outdir>
Prerequisites:
- Unix based system (Ubuntu, OSX, etc)
- Install git if required: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git.
- Git clone the repository and
make: - To check if there's update do
git pull
git clone git@github.com:chedinlab/rlooper_sim.git
cd rlooper_sim
make
cd rlooper_sim
# Example, no nick
bin/rlooper_sim --i example/pFC9_small.fa --outdir example/pFC9_small_outdir
# Example, no nick, with junc energy -a 20 and sigma -0.07 (7%), getting peaks that are at least 50bp
bin/rlooper_sim --i example/pFC9_small.fa --outdir example/pFC9_small_outdir_a20_sigmamin7_minlen50 --a 20 --sigma -0.070 --minlength 50
# Example as above, but with nick at 300bp position and nicklen 1
bin/rlooper_sim --i example/pFC9_small.fa --outdir example/pFC9_small_outdir_a20_sigmamin7_minlen50_nick300_nicklen1 --a 20 --sigma -0.070 --minlength 50 --nick 300 --nicklen 1
Usage: rlooper_sim --i <fastaFile.fa> --outdir <outdir> --o <outprefix>
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Options
--i/--fasta [file.fa] : fasta input.fa. IMPORTANT: HEADER HAS TO BE IN THIS FORMAT (Example from 1-3908):
>mydef range=mygene:1-3908 5'pad=0 3'pad=0 strand=- repeatMasking=none
ACGTCGT...
--outdir [string] : output directory
--N [int] : specifies length of superhelical region in bp [1500]
--a [int] : junction energy in kcal/mol, for B DNA it's 10-11 [10]
--sigma [float] : superhelical density of the region [-0.07]
--minlength [int] : minimum rloop peak length in bp [50]
--nick [int] : specifies the ssDNA nick region [N/A]
--nicklen [int] : specifies the length of ssDNA nick region [N/A]
--beg [int] : get seq only from this bp from the input fasta [1]
--end [int] : get seq only until this bp from the input fasta [all]
--help/--h : print this message
--seed : Seed for RNG [42]
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Additional settings can be found in settings.ini file, but be careful as changing this could break the software
The original version of this software (rlooper) is developed by Robert Stolz (rstolzATucdavis.edu) at https://github.com/chedinlab/rlooper/ rlooper_sim was developed and maintained by Stella R Hartono (srhartonoATucdavis.edu)
Development of this software was funded in part by NIH grant GM120607 and NSF CAREER grant DMS1057284.
rlooper_sim
Copyright (C) 2025 Stella R Hartono and Robert Stolz
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
The license can be found at https://www.gnu.org/licenses/gpl-3.0.en.html.
By downloading or using this software, you agree to the terms and conditions of the license.