Open jpearl01 opened 1 year ago
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
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
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:
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