1. Introduction<\/a> 28 April 2025: version 1.1.0 (click to download)<\/a><\/strong><\/p>\n 11 July 2022: version 1.0.1 (click to download)<\/a><\/strong><\/p>\n Circall is a novel method for fast and accurate discovery of circular RNAs from paired-end RNA-sequencing data. The method controls false positives by two-dimensional local false discovery method and employs quasi-mapping for fast and accurate alignments. The details of Circall are described in its manuscript. In this page, we present the Circall tool and how to use it.<\/p>\n Circall is implemented in R and C++. We acknowledge for materials from Sailfish, Rapmap and other tools used in this software.<\/p>\n Circall requires<\/p>\n The current Circall version was tested on the human genome, transcriptome with ensembl annotation version GRCh37.75. Specifically, the following files are required:<\/p>\n The latest version and information of Circall is updated at:\u00a0https:\/\/www.meb.ki.se\/sites\/biostatwiki\/circall\/<\/a><\/p>\n If you use the binary verion of Circall:<\/strong><\/p>\n If you want to build Circall from sources:<\/strong><\/p>\n -After the installation is finished, remember to add the paths of lib folder and bin folder to LD_LIBRARY_PATH and PATH<\/p>\n Install Circall from sources in Ubuntu<\/strong><\/p>\n The BSJ reference database for Homo_sapiens.GRCh37.75 was generated and able to download from Homo_sapiens.GRCh37.75_BSJ_sequences.fa<\/a>. This file was generated by the following command:<\/p>\n Now, all annotation data are generated and ready to run Circall.<\/strong><\/em><\/p>\n Suppose sample_01_1.fasta and sample_01_2.fasta are the input fastq files. For convenience, we prepared a toy example to test the pipeline, which can be downloaded here:<\/p>\n Circall can be run in one command wrapped in a bash script:<\/p>\n Annotation data:<\/strong><\/em><\/p>\n Input data:<\/strong><\/em><\/p>\n Other parameters:<\/strong><\/em><\/p>\n The main output of Circall is provided in *_Circall_final.txt. In this file, each row indicates one circular RNA, and the information of one circular RNA is presented in 8 columns:<\/p>\n In this section, we provide a practical example of using Circall in a copy-paste manner for a Hs68 cell line dataset.<\/p>\n In our experience, it takes around 8 CPU hours with a single CPU in total to complete.<\/p>\n<\/div>\n Circall simulator is a tool integrated in Circall to generate RNA-seq data of both circRNA and tandem RNA. The source codes are provided in R\/Circall_simulator.R of the Circall tool. The main function of the simulator is Circall_simulator() which is able to be run in R console. This function requires the following parameters:<\/span><\/p>\n For an illustration of using Circall simulator, we provide in this section a toy example. Suppose your current working directory contains the installed Circall and the annotation data. First, we need to load the functions of the simulator into your R console:<\/p>\n Then we create objects circInfo<\/strong> and tandemInfo<\/strong> containing the information of CircRNAs and tandem RNAs<\/p>\n Finally, we run the simulator:<\/p>\n You can find in the “.\/simulation_test” that contains the outputs including:<\/p>\n Circall uses GNU General Public License GPL-3.<\/p>\n A fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data Contents 1. Introduction 2. Download and installation 3. Prepare BSJ reference database and annotation files 4. Indexing transcriptome and BSJ reference database 5. Run Circall pipeline 6. A practical copy-paste example of running Circall 7. Circall simulator Update news 28 April […]<\/p>\n","protected":false},"author":20,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-1261","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/posts\/1261","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/users\/20"}],"replies":[{"embeddable":true,"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/comments?post=1261"}],"version-history":[{"count":27,"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/posts\/1261\/revisions"}],"predecessor-version":[{"id":1378,"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/posts\/1261\/revisions\/1378"}],"wp:attachment":[{"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/media?parent=1261"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/categories?post=1261"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-json\/wp\/v2\/tags?post=1261"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\n2. Download and installation<\/a>
\n3. Prepare BSJ reference database and annotation files<\/a>
\n4. Indexing transcriptome and BSJ reference database<\/a>
\n5. Run Circall pipeline<\/a>
\n6. A practical copy-paste example of running Circall<\/a>
\n7. Circall simulator<\/a><\/p>\n<\/a>Update news<\/h2>\n
\n
\n
<\/a>19 June 2020: version 0.1.0 (click to download)<\/a><\/h4>\n
\n
<\/a>1. Introduction<\/h2>\n
<\/a>Software requirements:<\/h3>\n
\n
<\/a>Annotation reference<\/h3>\n
\n
\n
<\/a>Versions<\/h3>\n
<\/a>2. Download and installation<\/h2>\n
\n
wget --no-check-certificate -O Circall_v0.1.0_linux_x86-64.tar.gz https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-content\/uploads\/sites\/4\/2021\/04\/Circall_v0.1.0_linux_x86-64.tar_.gz<\/pre>\n<\/div>\n
\n
tar -xzvf Circall_v0.1.0_linux_x86-64.tar.gz<\/pre>\n<\/div>\n
\n
cd<\/span> Circall_v0.1.0_linux_x86-64\nbash config.sh\ncd<\/span> ..<\/pre>\n<\/div>\n\n
export<\/span> LD_LIBRARY_PATH=\/path\/to\/Circall_v0.1.0_linux_x86-64\/linux\/lib:$LD_LIBRARY_PATH<\/span>\nexport<\/span> PATH=\/path\/to\/Circall_v0.1.0_linux_x86-64\/linux\/bin:$PATH<\/span><\/pre>\n<\/div>\n\n
export<\/span> LD_LIBRARY_PATH=$PWD<\/span>\/Circall_v0.1.0_linux_x86-64\/linux\/lib:$LD_LIBRARY_PATH<\/span>\nexport<\/span> PATH=$PWD<\/span>\/Circall_v0.1.0_linux_x86-64\/linux\/bin:$PATH<\/span><\/pre>\n<\/div>\n\n
wget --no-check-certificate -O Circall_v0.1.0.tar.gz https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-content\/uploads\/sites\/4\/2021\/04\/Circall_v0.1.0.tar_.gz\ntar -xzvf Circall_v0.1.0.tar.gz\ncd<\/span> Circall_v0.1.0\nbash config.sh<\/pre>\n<\/div>\n\n
DBOOST_ROOT=\/path\/to\/boostDir\/ DTBB_INSTALL_DIR=\/path\/to\/tbbDir\/ DCMAKE_INSTALL_PREFIX=\/path\/to\/Circall_home bash install.sh<\/pre>\n<\/div>\n
export<\/span> LD_LIBRARY_PATH=\/path\/to\/Circall_home\/lib:$LD_LIBRARY_PATH<\/span>\nexport<\/span> PATH=\/path\/to\/Circall_home\/bin:$PATH<\/span><\/pre>\n<\/div>\n##########################\n### This contain scripts in the copy-and-paste manner (line-by-line) to install Circall from source codes\n### The scripts have been successfully tested in Ubuntu 16, 19 and 20.\n\n##########################\n### download Circall\nwget wget --no-check-certificate -O Circall_v0.1.0.tar.gz https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-content\/uploads\/sites\/4\/2021\/04\/Circall_v0.1.0.tar_.gz\ntar -xzvf Circall_v0.1.0.tar.gz\ncd Circall_v0.1.0\n\n#config to run Circall\nbash config.sh\n\n### install boost_1_55_0\nwget http:\/\/sourceforge.net\/projects\/boost\/files\/boost\/1.58.0\/boost_1_58_0.tar.gz\ntar -xvzf boost_1_58_0.tar.gz\ncd boost_1_58_0\n\nsudo apt-get update\nsudo apt-get install build-essential g++ python-dev autotools-dev libicu-dev build-essential libbz2-dev libboost-all-dev\nsudo apt-get install aptitude\naptitude search boost\n\n.\/bootstrap.sh --prefix=boost_1_58_0_build\n.\/b2\n.\/b2 install\n\n#The Boost C++ Libraries were successfully built!\n#add the lib and folder to paths\nexport LD_LIBRARY_PATH=$PWD\/boost_1_58_0_build\/stage\/lib:$LD_LIBRARY_PATH\nexport PATH=$PWD\/boost_1_58_0_build:$PATH\n\n\n### install tbb44_20160526oss\ncd ..\nwget https:\/\/www.threadingbuildingblocks.org\/sites\/default\/files\/software_releases\/source\/tbb44_20160526oss_src_0.tgz\ntar xvf tbb44_20160526oss_src_0.tgz\nsudo apt-get install libtbb-dev\n\n### install cmake for ubuntu: cmake 3.5.1\nsudo apt install cmake\n### install curl\nsudo apt install curl\n### install autoconf\nsudo apt-get install autoconf\n### install zlib\nsudo apt install zlib1g-dev\nsudo apt install zlib1g\n### update all installations\nsudo apt-get update\n\n### install Circall\nDBOOST_ROOT=$PWD\/boost_1_58_0\/boost_1_58_0_build\/ DTBB_INSTALL_DIR=$PWD\/tbb44_20160526oss\/ DCMAKE_INSTALL_PREFIX=Circall_0.1.0_build bash install.sh\n\n#The Circall_0.1.0 was successfully built!\n###########\n\n#add lib and bin folders to paths\nexport LD_LIBRARY_PATH=$PWD\/Circall_0.1.0_build\/lib:$LD_LIBRARY_PATH\nexport PATH=$PWD\/Circall_0.1.0_build\/bin:$PATH\n\n#done\n###########<\/pre>\n<\/div>\n
<\/a>3. Prepare BSJ reference database and annotation files<\/h2>\n
<\/a>Download genome fasta, transcript fasta and gtf annotation files.<\/h3>\n
wget http:\/\/ftp.ensembl.org\/pub\/release-75\/fasta\/homo_sapiens\/dna\/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz\ngunzip Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz\nwget http:\/\/ftp.ensembl.org\/pub\/release-75\/fasta\/homo_sapiens\/cdna\/Homo_sapiens.GRCh37.75.cdna.all.fa.gz\ngunzip Homo_sapiens.GRCh37.75.cdna.all.fa.gz\nwget http:\/\/ftp.ensembl.org\/pub\/release-75\/gtf\/homo_sapiens\/Homo_sapiens.GRCh37.75.gtf.gz\ngunzip Homo_sapiens.GRCh37.75.gtf.gz<\/pre>\n<\/div>\n
<\/a>Create sqlite<\/h3>\n
Rscript Circall_v0.1.0_linux_x86-64\/R\/createSqlite.R Homo_sapiens.GRCh37.75.gtf Homo_sapiens.GRCh37.75.sqlite<\/pre>\n<\/div>\n
<\/a>Create BSJ reference database<\/h3>\n
Rscript Circall_v0.1.0_linux_x86-64\/R\/buildBSJdb.R gtfSqlite=Homo_sapiens.GRCh37.75.sqlite genomeFastaFile=Homo_sapiens.GRCh37.75.dna.primary_assembly.fa bsjDist=250 maxReadLen=150 output=Homo_sapiens.GRCh37.75_BSJ_sequences.fa<\/pre>\n<\/div>\n
<\/a>4. Indexing transcriptome and BSJ reference database<\/h2>\n
<\/a>Index transcriptome<\/h3>\n
Circall_v0.1.0_linux_x86-64\/linux\/bin\/TxIndexer -t Homo_sapiens.GRCh37.75.cdna.all.fa -o IndexTranscriptome<\/pre>\n<\/div>\n
<\/a>Index BSJ reference database<\/h3>\n
Circall_v0.1.0_linux_x86-64\/linux\/bin\/TxIndexer -t Homo_sapiens.GRCh37.75_BSJ_sequences.fa -o IndexBSJ<\/pre>\n<\/div>\n
<\/a>5. Run Circall pipeline<\/h2>\n
wget https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-content\/uploads\/sites\/4\/2021\/07\/sample_01_1.fasta_.gz\nwget https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-content\/uploads\/sites\/4\/2021\/07\/sample_01_2.fasta_.gz<\/pre>\n<\/div>\n
bash Circall_v0.1.0_linux_x86-64\/Circall.sh -genome Homo_sapiens.GRCh37.75.dna.primary_assembly.fa -gtfSqlite Homo_sapiens.GRCh37.75.sqlite -txFasta Homo_sapiens.GRCh37.75.cdna.all.fa -txIdx IndexTranscriptome -bsjIdx IndexBSJ -dep Circall_v0.1.0_linux_x86-64\/Data\/Circall_depdata_human.RData -read1 sample_01_1.fasta.gz -read2 sample_01_2.fasta.gz -p 4 -tag testing_sample -c FALSE -o Testing_out<\/pre>\n<\/div>\n
<\/a>Inputs and parameters<\/h3>\n
\n
\n
\n
Output<\/h3>\n
\n
<\/a>6. A practical copy-paste example of running Circall<\/h2>\n
<\/a>Download and install Circall<\/h3>\n
wget --no-check-certificate -O Circall_v0.1.0_linux_x86-64.tar.gz https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-content\/uploads\/sites\/4\/2021\/04\/Circall_v0.1.0_linux_x86-64.tar_.gz<\/pre>\n<\/div>\n
\n
tar -xzvf Circall_v0.1.0_linux_x86-64.tar.gz<\/pre>\n<\/div>\n
\n
cd<\/span> Circall_v0.1.0_linux_x86-64\nbash config.sh\ncd<\/span> ..<\/pre>\n<\/div>\n\n
export<\/span> LD_LIBRARY_PATH=$PWD<\/span>\/Circall_v0.1.0_linux_x86-64\/linux\/lib:$LD_LIBRARY_PATH<\/span>\nexport<\/span> PATH=$PWD<\/span>\/Circall_v0.1.0_linux_x86-64\/linux\/bin:$PATH<\/span><\/pre>\n<\/div>\n<\/a>Download genome fasta, transcript fasta and BSJ databases and annotation file.<\/h3>\n
# genome from ENSEMBL website<\/span>\nwget http:\/\/ftp.ensembl.org\/pub\/release-75\/fasta\/homo_sapiens\/dna\/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz\ngunzip Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz\n\n# cDNA (transcript) and Gene annotation (gft) from ENSEMBL website<\/span>\nwget http:\/\/ftp.ensembl.org\/pub\/release-75\/fasta\/homo_sapiens\/cdna\/Homo_sapiens.GRCh37.75.cdna.all.fa.gz\ngunzip Homo_sapiens.GRCh37.75.cdna.all.fa.gz\nwget http:\/\/ftp.ensembl.org\/pub\/release-75\/gtf\/homo_sapiens\/Homo_sapiens.GRCh37.75.gtf.gz\ngunzip Homo_sapiens.GRCh37.75.gtf.gz\n\n# pre-built BSJ databases from Circall website<\/span>\nwget https:\/\/www.meb.ki.se\/sites\/biostatwiki\/wp-content\/uploads\/sites\/4\/files\/circall\/Homo_sapiens.GRCh37.75_BSJ_sequences.fa.gz\ngunzip Homo_sapiens.GRCh37.75_BSJ_sequences.fa.gz\n\n# Genarate Sqlite annotation<\/span>\nRscript Circall_v0.1.0_linux_x86-64\/R\/createSqlite.R Homo_sapiens.GRCh37.75.gtf Homo_sapiens.GRCh37.75.sqlite\n\n<\/pre>\n<\/div>\n<\/a>Index transcriptome<\/h3>\n
Circall_v0.1.0_linux_x86-64\/linux\/bin\/TxIndexer -t Homo_sapiens.GRCh37.75.cdna.all.fa -o IndexTranscriptome<\/pre>\n<\/div>\n
<\/a>Index BSJ reference database<\/h3>\n
Circall_v0.1.0_linux_x86-64\/linux\/bin\/TxIndexer -t Homo_sapiens.GRCh37.75_BSJ_sequences.fa -o IndexBSJ<\/pre>\n<\/div>\n
<\/a>Download Hs68 cell line RNA-seq data<\/h3>\n
wget ftp:\/\/ftp.sra.ebi.ac.uk\/vol1\/fastq\/SRR444\/SRR444975\/SRR444975_1.fastq.gz\nwget ftp:\/\/ftp.sra.ebi.ac.uk\/vol1\/fastq\/SRR444\/SRR444975\/SRR444975_2.fastq.gz<\/pre>\n<\/div>\n
<\/a>Run Circall<\/h3>\n
bash Circall_v0.1.0_linux_x86-64\/Circall.sh -genome Homo_sapiens.GRCh37.75.dna.primary_assembly.fa -gtfSqlite Homo_sapiens.GRCh37.75.sqlite -txFasta Homo_sapiens.GRCh37.75.cdna.all.fa -txIdx IndexTranscriptome -bsjIdx IndexBSJ -dep Circall_v0.1.0_linux_x86-64\/Data\/Circall_depdata_human.RData -read1 SRR444975_1.fastq.gz -read2 SRR444975_2.fastq.gz -p 4 -tag testing_sample -o SRR444975<\/pre>\n
<\/a>7.\u00a0 Circall simulator<\/h2>\n
<\/a>Introduction<\/h3>\n
<\/a>Parameter setting:<\/h3>\n
\n
<\/a>A toy example for using Circall simulator<\/h3>\n
source(\"<\/span>Circall_v0.1.0_linux_x86-64\/R\/Circall_simulator.R\"<\/span><\/span>)\n<\/pre>\n<\/div>\nChr = c(7,7,3,5,17,4,7,1,3,1,17,12,14,10,18,17,5,20,16,17)\n\nstart_EXONSTART = c(131113792,99795401,172363413,179296769,36918664,151509200,2188787,51906019,57832924,225239153,76187051,111923075,104490906,101556854,196637,21075331,74981032,60712420,56903641,80730328)\n\nend_EXONEND = c(131128461,99796580,172365904,179315312,36918758,151509336,2270359,51913807,57882659,225528403,76201599,111924628,104493276,101572901,199316,21087123,74998635,60716000,56904648,80772810)\n\nGENEID = c(\"ENSG00000128585\",\"ENSG00000066923\",\"ENSG00000144959\",\"ENSG00000197226\",\"ENSG00000108294\",\"ENSG00000198589\",\"ENSG00000002822\",\"ENSG00000085832\",\"ENSG00000163681\",\"ENSG00000185842\",\"ENSG00000183077\",\"ENSG00000204842\",\"ENSG00000156414\",\"ENSG00000023839\",\"ENSG00000101557\",\"ENSG00000109016\",\"ENSG00000152359\",\"ENSG00000101182\",\"ENSG00000070915\",\"ENSG00000141556\")\n\nset.seed(2021)\ncCount = sample(2:2000,20)\nFPKM = rep(0,20)\n\nBSJ_info = data.frame(Chr = Chr, start_EXONSTART = start_EXONSTART, end_EXONEND = end_EXONEND, GENEID = GENEID, cCount = cCount, FPKM = FPKM)\n\ncircSet=c(1:15)\ncircInfo = BSJ_info[circSet,]\ntandemInfo = BSJ_info[-circSet,]<\/pre>\n<\/div>\n
simulation = Circall_simulator(circInfo = circInfo, tandemInfo = tandemInfo, useFPKM=FALSE, out_name = \"Tutorial\", gtfSqlite = \"Homo_sapiens.GRCh37.75.sqlite\", genomeFastaFile = \"Homo_sapiens.GRCh37.75.dna.primary_assembly.fa\", txFastaFile = \"Homo_sapiens.GRCh37.75.cdna.all.fa\", out_dir= \".\/simulation_test\")\n<\/pre>\n<\/div>\n
\n
8. License<\/h2>\n
9. References<\/h2>\n<\/div>\n