Pulling Oligos from Prebuilt dataset

[jpearl01]

Hello,

I'm trying to get guide RNAs out of CasOligo. In Supplemental file Figure S4 several guide RNAs are listed. Is it possible to get the sequence of these guide RNAs from CasOligo? For example, if I try to get the sequence sgRNA_044409 - what command do I need to execute? I have tried:

library(CasOligo)

search.db.byid(query="sgRNA_044409", cas="Cas9")

But this just gives me a warning:
Warning: attempt to set 'col.names' ignored

Should this work, or am I doing something wrong?

Thanks,
~josh

[jpearl01]

Something is definitely wrong. Not sure what is happening, but I can't get the example to run. here is the entirety of my script (I'm running this in:
RStudio 2023.03.1+446 "Cherry Blossom" Release (6e31ffc3ef2a1f81d377eeccab71ddc11cfbd29e, 2023-05-09) for windows

My R version is:

               _                                
platform       x86_64-w64-mingw32               
arch           x86_64                           
os             mingw32                          
crt            ucrt                             
system         x86_64, mingw32                  
status                                          
major          4                                
minor          2.2                              
year           2022                             
month          10                               
day            31                               
svn rev        83211                            
language       R                                
version.string R version 4.2.2 (2022-10-31 ucrt)
nickname       Innocent and Trusting            

The script is:

knitr::opts_chunk$set(echo = TRUE)
#Install pacman if it is not already installed, then load
if (!require("pacman")) install.packages("pacman", "CRAN")
library(pacman)

#use pacman to unload current environment..
pacman::p_unload(pacman::p_loaded(), character.only = TRUE)

if (!require("devtools"))
  install.packages("devtools")
devtools::install_github("kevinzhongxu/CasOligo", auth_token = "HIDDEN")
library(CasOligo)


search.db.byid(query="sgRNA_044409", cas="Cas9")

I get these warnings:

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated,
    eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

The following object is masked from ‘package:grid’:

    pattern

The following object is masked from ‘package:base’:

    strsplit


Attaching package: ‘ape’

The following object is masked from ‘package:Biostrings’:

    complement

Warning: attempt to set 'col.names' ignored

Any help would be appreciated!
thanks,
~josh

[jpearl01]

Alright, if I just load in R, (not Rstudio) I can execute the example command, and it outputs a csv file that looks like this:

oligo.ID,gRNA-target-sequence-oligo,strand,start,end,pam.seq,hits.to.microeukaryotes,microeukaryotes.target.range,host.to.target,nbr.host.taxa.targeted
probe_022593,ACGTGAGGTAATGATTAAGA,forward,280,299,GGG,0,0,DQ300016.1.1726___7..1726___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Annelida;D_6__Xenosiphon branchiatus;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,280,299,GGG,0,0,DQ300005.1.1769___1..1769___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Annelida;D_6__Sipunculus nudus marine worm;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,285,304,GGG,0,0,JN869397.1.1777___1..1777___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Annelida;D_6__Spinculida;D_7__Nephasoma columbaris;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,289,308,GGG,0,0,AF120522.1.1804___9..1804___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Mollusca;D_6__Scaphopoda;D_7__Dentaliidae;D_8__Dentalium pilsbryi;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,281,300,GGG,0,0,JN974518.1.1768___1..1743___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Mollusca;D_6__Bivalvia;D_7__Arcoida;D_8__Arca navicularis;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,280,299,GGG,0,0,DQ300008.1.1767___9..1767___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Annelida;D_6__Sipunculus nudus marine worm;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,278,297,GGG,0,0,HQ728922.1.1711___15..1711___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Annelida;D_6__Enchytraeidae;D_7__Komarekiona eatoni;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,278,297,GGG,0,0,JF293046.1.1772___9..1772___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Nemertea;D_6__Baseodiscus sp. 2 SA-2011;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,289,308,GGG,0,0,AJ389663.1.1744___1..1744___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Mollusca;D_6__Scaphopoda;D_7__Dentaliidae;D_8__Antalis perinvoluta;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10
probe_022593,ACGTGAGGTAATGATTAAGA,forward,279,298,GGG,0,0,AB211066.1.1750___1..1748___D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa;D_4__Animalia;D_5__Urochordata;D_6__Ascidiacea;D_7__Botryllus schlosseri;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__,10

So that seems to be working. If I change the search term from the name in the paper "sgRNA_044409" to "probe_044409" I do get outputs. Are these terms equivalent?

Thanks,
~josh