Thanks for your work of circRNA.

1. 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.

2. gff in line 37 of showOverview.R should be replaced with genomegff.

3. 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 excellent work!

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 Rcirc

install_github('PSSUN/Rcirc')
library(Rcirc)

I'm following the manual from https://rcirc-doc.readthedocs.io/en/latest/Usage/Usage.html

we will repair this error in 2 hours

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！！！

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