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View Code? Open in Web Editor NEWR language based circRNA visualization toolbox
License: GNU General Public License v3.0
R language based circRNA visualization toolbox
License: GNU General Public License v3.0
- In the showOverview function, the Ribo-seq and RNA-seq files should be inputted in bed format, and the manual page was misspelled as bam format.
- gff in line 37 of showOverview.R should be replaced with genomegff.
- In the section on 'Analysis the reads mapping on sequences', the makeGenome() function should be changed to randomSeq()
sunmitted by: Ludong Yang
Thanks for your work of circRNA.
Hi, I'm getting an error when running TranslateCirc
ILLUMINACLIP: Using 0 prefix pairs, 138 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 93462704 Surviving: 92983770 (99.49%) Dropped: 478934 (0.51%)
TrimmomaticSE: Completed successfully
sh: bowtie: command not found
sh: bowtie: command not found
sh: STAR: command not found
Error in system("rm -rf", tmp) : 'intern' must be TRUE or FALSE
In addition: Warning messages:
1: In system(gindex_command) : error in running command
2: In system(index_command) : error in running command
3: In system(rindex_command) : error in running command
4: In system(remove_command) : error in running command
5: In system(remove_liner_command) : error in running command
6: In system(map_command) : error in running command
In my modules loaded,
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicAlignments", force = TRUE)
install.packages('Biostrings')
BiocManager::install('GenomicAlignments')
BiocManager::install('GenomicFeatures')
BiocManager::install('GenomicRanges', force = TRUE)
install.packages('RColorBrewer')
install.packages('circlize')
install.packages('dplyr')
install.packages('ggplot2')
install.packages('grid')
install.packages('gtable')
install.packages('stringr')
BiocManager::install('Rbowtie2', force = TRUE)
install.packages('usethis', force = TRUE)
install.packages('devtools')
library(devtools)
library(Rbowtie2)
install_github('PSSUN/Rcirc')
library(Rcirc)
I'm following the manual from https://rcirc-doc.readthedocs.io/en/latest/Usage/Usage.html
I am trying to install this package, but gives me the following error:
Error : (converted from warning) unable to re-encode 'rCirc.R' line 52
ERROR: unable to collate and parse R files for package 'Rcirc'.
Error: Failed to install 'Rcirc' from GitHub:
(converted from warning) installation of package ‘C:/Users/aayus/AppData/Local/Temp/RtmpspA0yH/file2f1ccbd213e/Rcirc_0.1.0.tar.gz’ had non-zero exit status
Thanks for your excellent work!
out='/storage/zuozd/rcirc/test/out.bam'
fastq='"/storage/zuozd/circcode/rice/ZH11_1_trans.fastq"'
fastq="/storage/zuozd/circcode/rice/ZH11_1_trans.fastq"
adapter="/storage/zuozd/circcode/rice/adapter_rice.fa"
trimmomatic="/storage/zuozd/circcode/CircCode-master/requiredSoft/trimmomatic-0.38.jar"
genome="/storage/zuozd/genome/oryza_sativa_Japonica/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa"
tmp='/storage/zuozd/rcirc/test/temp/temp.file'
circgenome="/storage/zuozd/circcode/rice/osa_isoform.fasta"
rRNA="/storage/zuozd/circcode/CircCode-master/test-ara/plant-rrna.fasta"
TranslateCirc(out,fastq,adapter,trimmomatic,genome,tmp,circgenome,rRNA)
Error in TranslateCirc(out, fastq, adapter, trimmomatic, genome, tmp, :
找不到对象'geneome'
TranslateCirc(out,fastq,adapter,trimmomatic,genome,tmp,circgenome,rRNA)
Error in TranslateCirc(out, fastq, adapter, trimmomatic, genome, tmp, :
找不到对象'geneome'
TranslateCirc(out,fastq,adapter,trimmomatic,genome,tmp,circgenome,rRNA)
Error in TranslateCirc(out, fastq, adapter, trimmomatic, genome, tmp, :
找不到对象'geneome'
请问这个问题怎么解决。谢谢!!!
we will repair this error in 2 hours
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