ProbeSHIFTR

Oligonucleotide probe designer for Selective RNase-H-mediated Interactome Framing for Target RNA Regions (SHIFTR)

Design of oligo sequences for the publication

SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells.

Jens Aydin, Alexander Gabel, Sebastian Zielinski, Sabina Ganskih, Nora Schmidt, Christina R. Hartigan, Monica Schenone, Steven A. Carr, and Mathias Munschauer.

Requirements

• JavaSE-14
• R (tested on R-4.2.1)
• required R packages:
  • readr
  • data.table
  • rtracklayer
  • GenomicRanges
  • IRanges
  • tidyr
  • seqinr
  • ggplot2
• install BLAT
• java, R, BLAT and all required packages can be found in environmental.yaml

Installation

Use conda to create an environment for ProbeSHIFTR:

conda env create -f environment.yaml

Acitvate ProbeSHIFTR environment:

conda activate probeshiftr

Usage

usage: java -jar ProbeSHIFTR.jar [-bf <arg>] [-blat <arg>] [-cw] [-d
       <arg>] [-D <arg>] [-f <arg>] [-g <arg>] [-h] [-irk] [-l <arg>]
       [-log] [-match <arg>] [-n <arg>] [-nm <arg>] [-o <arg>] [-p <arg>]
       [-pbl <arg>] [-r <arg>] [-rbl <arg>] [-rmf <arg>] [-rscript <arg>]
       [-s] [-score <arg>] [-t <arg>]
 -bf,--bases2filter <arg>               bases to filter for polybases in
                                        oligos (Default: ACGT)
 -blat,--blat-path <arg>                path to BLAT executable (Default:
                                        assumed to be in the environmental
                                        variable PATH)
 -cw,--check-within-target              check for homologies within target
                                        sequence (Default: false)
 -d,--database-fasta <arg>              database sequence file for BLAT
                                        searches (e.g. genome.fasta)
 -D,--database-dir <arg>                directory containing fasta files
                                        for BLAT searches
 -f,--fragment-size <arg>               if gaps between oligos are longer
                                        than the fragment size then oligos
                                        with too many off-targets are used
                                        to fill these gaps (Default: 200)
 -g,--gtf-files <arg>                   gtf/gff annotation files to
                                        consider protein-coding exonic
                                        off-target regions (separated by
                                        semicolon without spaces e.g.
                                        anno1.gtf;anno2.gtf)
 -h,--help                              print this message
 -irk,--include-repetitive-kmers        include repetitive kmers (Default:
                                        false)
 -l,--oligo-length <arg>                length of antisense oligos
 -log,--log-file                        write log file to evaluate
                                        sequence complexity filters
                                        (Default: false)
 -match,--min-match <arg>               minimal matches for BLAT searches
                                        (Default: 1)
 -n,--include-n <arg>                   include N in repeat filtering
                                        (Default: true)
 -nm,--n-repeats <arg>                  relative freuqnecies of N repeats
                                        in oligos (Default: 0.001)
 -o,--output-dir <arg>                  directory to store oligo designs
                                        and temporary files (e.g. BLAT
                                        results)
 -p,--processes <arg>                   number of parallel
                                        threads/processes to run BLAT
                                        comparisons
 -pbl,--polybase-length <arg>           relative length of polybases
                                        within oligo (Default: 0.8)
 -r,--max-repeats <arg>                 maximal percetage of repeats
                                        (Default: 0.07)
 -rbl,--repeat-length-polybases <arg>   length of polybase repreats within
                                        sequences (Default: 15)
 -rmf,--repeat-masking-format <arg>     repeats masked with upper or lower
                                        cases or no masking in data
                                        (lower, upper; Default: lower)
 -rscript,--rscript-path <arg>          path to Rscript executable
                                        (Default: assumed to be in the
                                        environmental variable PATH)
 -s,--get-sense                         create sense oligos (Default:
                                        false)
 -score,--min-score <arg>               mininmal score for BLAT searches
                                        (Default: 10)
 -t,--target-fasta <arg>                fasta containing target
                                        sequence(s)