Circall: A fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data

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IMPORTANT NOTE: I tested with 45GB of RAM and 32 CPU cores and recommend a minimum of 45 GB of RAM to obtain stable results for Circall.

Update news

11 July 2022: version 1.0.1

Some changes in C++ binary (rebuild the software).

06 July 2022: version 1.0.0

Re-organization of the software package => user-friendly version with Docker.
Speed up file reading in R with data.table.
Fix bugs in hg38 annotation.
Default option "-td" changed to FALSE.
Output format with an additional column: junction_FPM - junction fragment per million .i.e, junction_fragment_count normalized by million fragment unit.

NOTE:

Tutorial has been changed for Docker running tutorial in this version.
An old version can be found in the sub-directory Circall_v0.1.0.

19 June 2020: version 0.1.0

Instruction how to build the software from source can be found at: https://www.meb.ki.se/sites/biostatwiki/circall/

First submission

1. Introduction

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.

Software requirements:

Docker

Annotation reference

Circall requires:

1) a fasta file of transcript sequences and a gtf file of transcript annotation: can be downloaded from public repositories such as Ensembl (ensembl.org) 2) a genome file of transcript sequences and a gtf file of transcript annotation: can be downloaded from public repositories such as Ensembl (ensembl.org) 3) a RData file of supporting annotation: A description of how to create the RData file for new annotation versions or species is available in the following section. 4) a back-splicing-junction (BSJ) reference sqeuences: A description of how to create the BSJ reference sqeuences for new annotation versions or species is available in the following section.

Current Circall version was tested on the human genome (hg18 and hg38). Detail tutorials are in section 3 (hg19), and section 4 (hg38).

2. Download and installation

The esiest way to install and run Circall is using our pre-buit Docker immage:

# pull circall docker image:
docker pull ndatth/circall:v1.0.1

# test your docker
docker run --rm ndatth/circall:v1.0.1 Circall.sh

Expected output is:

--------------------------------------------------------------------------
                     _
            _____   (_)   _____  _____   __        __      __
           / ___/  / /   / ___/ / ___/  /  \      / /     / /
          / /__   / /   / /    / /__   / __ \    / /__   / /__
          \___/  /_/   /_/     \___/  /_/  \_\  /_/__/  /_/__/

---------------------------------------------------------------------------
                     Checking arguments ....
---------------------------------------------------------------------------

Usage:
./Circall.sh
    -genome [genome in fasta format]
    -gtfSqlite [genome annotation in Sqlite format]
    -txFasta [transcripts (cDNA) in fasta format]
    -txIdx [quasi-index of txFasta]
    -bsjIdx [quasi-index of BSJ reference fasta file]
    -read1 [read1 fastq.gz file]
    -read2 [read2 fastq.gz file]
    -thread [number of thread]
    -tag [tag name]
    -td [TRUE/FALSE value, defaut is FALSE]
    -c[TRUE/FALSE value, defaut is TRUE]
    -o [output folder]

If you want to build Circall from sources: Please prefer to our wiki webpage https://www.meb.ki.se/sites/biostatwiki/circall for detail instruction

3. Tutorial for human genome hg19 (GRCh37), annotation version 75.

3.1 Prepare BSJ reference database and Sqlite annotation file

Download genome fasta, transcript fasta and gtf annotation files.

wget http://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
wget http://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.75.cdna.all.fa.gz
gunzip Homo_sapiens.GRCh37.75.cdna.all.fa.gz
wget http://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz
gunzip Homo_sapiens.GRCh37.75.gtf.gz

Create sqlite

You can generate the sqlite annotation database was generated and able to download from Homo_sapiens.GRCh37.75.sqlite. This file was generated by the following command:

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 createSqlite.R \
        data/Homo_sapiens.GRCh37.75.gtf \
        data/Homo_sapiens.GRCh37.75.sqlite

Create BSJ reference database

The BSJ reference database for Homo_sapiens.GRCh37.75 was generated and able to download from Homo_sapiens.GRCh37.75_BSJ_sequences.fa. This file was generated by the following command:

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 buildBSJdb.R \
        gtfSqlite=data/Homo_sapiens.GRCh37.75.sqlite \
        genomeFastaFile=data/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa \
        bsjDist=250 maxReadLen=150 \
        output=data/Homo_sapiens.GRCh37.75_BSJ_sequences.fa

3.2 Indexing transcriptome and BSJ reference database

Index transcriptome

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
# please uncompress your fa file (with gunzip) before indexing 
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 TxIndexer \
        -t data/Homo_sapiens.GRCh37.75.cdna.all.fa \
        -o data/IndexTranscriptome

Index BSJ reference database

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
# please uncompress your fa file (with gunzip) before indexing 
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 TxIndexer \
        -t data/Homo_sapiens.GRCh37.75_BSJ_sequences.fa \
        -o data/IndexBSJ

Now, you are ready to run Circall.

3.3 Run Circall pipeline

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:

wget https://github.com/datngu/Circall/releases/download/v0.1.0/sample_01_1.fasta.gz
wget https://github.com/datngu/Circall/releases/download/v0.1.0/sample_01_2.fasta.gz

Circall can be run in one command wrapped in a bash script:

docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 Circall.sh \
    -genome data/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa \
    -gtfSqlite data/Homo_sapiens.GRCh37.75.sqlite \
    -txFasta data/Homo_sapiens.GRCh37.75.cdna.all.fa \
    -txIdx data/IndexTranscriptome \
    -bsjIdx data/IndexBSJ \
    -dep Circall/Data/Circall_depdata_human.RData \
    -read1 data/sample_01_1.fasta.gz \
    -read2 data/sample_01_2.fasta.gz \
    -p 4 \
    -tag testing_sample \
    -c FALSE \
    -td FASLE \
    -o data/Testing_HG19_out

NOTED: sample depdata of Hela, HEK293, HS68 (cell-lines) are located in Docker immage, path: Circall/Data/Circall_depdata_human.RData

4. Tutorial for human genome hg38 (GRCh38), annotation version 106.

4.1 Prepare BSJ reference database and Sqlite annotation file

Download genome fasta, transcript fasta and gtf annotation files.

wget http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz -O Homo_sapiens.GRCh38.106.gtf.gz
wget http://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz -O Homo_sapiens.GRCh38.cdna.all.fa.gz
wget http://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz -O Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz

gunzip Homo_sapiens.GRCh38.106.gtf.gz
gunzip Homo_sapiens.GRCh38.cdna.all.fa.gz
gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz

Create sqlite

You can generate the sqlite annotation database was generated and able to download from Homo_sapiens.GRCh38.106.sqlite. This file was generated by the following command:

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 createSqlite.R \
        data/Homo_sapiens.GRCh38.106.gtf \
        data/Homo_sapiens.GRCh38.106.sqlite

Create BSJ reference database

The BSJ reference database for Homo_sapiens.GRCh38.106 was generated and able to download from Homo_sapiens.GRCh38.106_BSJ_sequences.fa. This file was generated by the following command:

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 buildBSJdb.R \
        gtfSqlite=data/Homo_sapiens.GRCh38.106.sqlite \
        genomeFastaFile=data/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
        bsjDist=250 maxReadLen=150 \
        output=data/Homo_sapiens.GRCh38.106_BSJ_sequences.fa

4.2 Indexing transcriptome and BSJ reference database

Index transcriptome

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
# please uncompress your fa file (with gunzip) before indexing 
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 TxIndexer \
        -t data/Homo_sapiens.GRCh38.cdna.all.fa \
        -o data/IndexTranscriptome

Index BSJ reference database

# assumming you are running unix and $PWD: is the path to directory that is mounted to docker containter as /data:
# please uncompress your fa file (with gunzip) before indexing 
docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 TxIndexer \
        -t data/Homo_sapiens.GRCh38.106_BSJ_sequences.fa \
        -o data/IndexBSJ

Now, you are ready to run Circall.

4.3 Run Circall pipeline

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:

wget https://github.com/datngu/Circall/releases/download/v0.1.0/sample_01_1.fasta.gz
wget https://github.com/datngu/Circall/releases/download/v0.1.0/sample_01_2.fasta.gz

Circall can be run in one command wrapped in a bash script:

docker run --rm -v $PWD:/data ndatth/circall:v1.0.1 Circall.sh \
    -genome data/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
    -gtfSqlite data/Homo_sapiens.GRCh38.106.sqlite \
    -txFasta data/Homo_sapiens.GRCh38.cdna.all.fa \
    -txIdx data/IndexTranscriptome \
    -bsjIdx data/IndexBSJ \
    -dep Circall/Data/Circall_depdata_human.RData \
    -read1 data/sample_01_1.fasta.gz \
    -read2 data/sample_01_2.fasta.gz \
    -p 4 \
    -tag testing_sample \
    -c FALSE \
    -td FASLE \
    -o data/Testing_HG38_out

NOTED: sample depdata of Hela, HEK293, HS68 (cell-lines) are located in Docker immage, path: Circall/Data/Circall_depdata_human.RData

5. Input, parameters, and output

Annotation data

Parameters	Description
gtfSqlite	genome in fasta format
Paragraph	genome annotation in Sqlite format
txFasta	transcripts (cDNA) in fasta format
txIdx	quasi-index of txFasta
bsjIdx	quasi-index of BSJ reference fasta file

Input data

Parameters	Description
read1	input read1: should be in gz format
read2	input read1: should be in gz format

Other parameters

Parameters	Description
dep	data contain depleted circRNAs: to specify the null data (depleted circRNA) for the two-dimensional local false discovery rate method. For convenience, we collect the null data from three human cell lines datasets Hela, Hs68, and Hek293 and provided in the tool: Circall_v0.1.0_linux_x86-64/Data/Circall_depdata_human.RData
p	the number of threads: Default is 4
tag	tag name of results: Default is “Sample”
td	generation of tandem sequences: TRUE/FALSE value, default is FASLE
c	clean intermediate data: TRUE/FALSE value, default is TRUE
o	output folder: Default is the current directory

Output

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:

Name	Description
chr	chromosome
start	start position
end	end position
geneID	gene name that the circRNA belongs to
circID	the ID of circRNA in the format “chrstartend”
junction_fragment_count	the number of fragment counts supporting the back-splicing-junction (BSJ)
junction_FPM	junction fragment per million .i.e, junction_fragment_count normalized by million fragment unit
median_circlen	the median length of the circular RNA
fdr	the false discovery rate computed from the two-dimensional local false discovery method

6. Circall simulator

Introduction

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 package. The main function of the simulator is Circall_simulator() which is able to be run in R console. This function requires the following parameters:

Parameter setting:

Name	Description
circInfo	a data frame that contains 6 columns which are: Chr, start_EXONSTART, end_EXONEND, GENEID, cCount and FPKM. Chr is chromosome name with formated as 1:22, X, Y, Mt. start_EXONSTART is starting position starting exon of circRNA, end_EXONEND is ending position ending exon of circRNA, GENEID is gene ID contains circRNA (used to get gene model), cCount are number of read pair want to generate for the target circRNA and FPKM are Fragments Per Kilobase of transcript per Million of target circRNAs. This is used to simulate circular RNAs
tandemInfo	a data frame similar to circInfo to simulate tandem RNAs. tandemInfo=NULL (the default value) to not simulate tandem RNAs
error_rate	sequencing error rate, the default value is 0.005
set.seed	set seed for reproducibility, the default value is 2018
gtfSqlite	path to your annotation file, Sqlite formated (generated by GenomicFeatures)
genomeFastaFile	path to your genome fasta file
txFastaFile	path to your transcript fasta file (cDNA)
out_name	prefix output folders, the default value is “Circall_simuation”
out_dir	the directory contains output, the default value is the current directory
lib_size	expected library size used when useFPKM=TRUE, the default value is NULL
useFPKM	boolean value to use FPKM or not, the default value is FALSE. When this useFPKM=TRUE, users need to set value for lib_size, and the simulator will use the abundance in column FPKM of circInfo/tandemInfo for simulation

A toy example for using Circall simulator

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:

source("/Circall_v1.0.0/R/Circall_simulator.R")

Then we create objects circInfo and tandemInfo containing the information of CircRNAs and tandem RNAs

Chr = c(7,7,3,5,17,4,7,1,3,1,17,12,14,10,18,17,5,20,16,17)

start_EXONSTART = c(131113792,99795401,172363413,179296769,36918664,151509200,2188787,51906019,57832924,225239153,76187051,111923075,104490906,101556854,196637,21075331,74981032,60712420,56903641,80730328)

end_EXONEND = c(131128461,99796580,172365904,179315312,36918758,151509336,2270359,51913807,57882659,225528403,76201599,111924628,104493276,101572901,199316,21087123,74998635,60716000,56904648,80772810)

GENEID = c("ENSG00000128585","ENSG00000066923","ENSG00000144959","ENSG00000197226","ENSG00000108294","ENSG00000198589","ENSG00000002822","ENSG00000085832","ENSG00000163681","ENSG00000185842","ENSG00000183077","ENSG00000204842","ENSG00000156414","ENSG00000023839","ENSG00000101557","ENSG00000109016","ENSG00000152359","ENSG00000101182","ENSG00000070915","ENSG00000141556")

set.seed(2021)
cCount = sample(2:2000,20)
FPKM = rep(0,20)

BSJ_info = data.frame(Chr = Chr, start_EXONSTART = start_EXONSTART, end_EXONEND = end_EXONEND, GENEID = GENEID, cCount = cCount, FPKM = FPKM)

circSet=c(1:15)
circInfo = BSJ_info[circSet,]
tandemInfo = BSJ_info[-circSet,]

Finally, we run the simulator:

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")

You can find in the “./simulation_test” that contains the outputs including:

simulation_setting: setting information of simulation of both circRNAs and tandem RNAs.
circRNA_data: RNA seq data of CircRNAs
tandem_data: RNA seq data of tandem RNA
fasta sequences of tandem RNAs
fasta sequences of circular RNAs

7. License

Circall uses GNU General Public License GPL-3.

8. Reference and citation

Nguyen, Dat Thanh, Quang Thinh Trac, Thi-Hau Nguyen, Ha-Nam Nguyen, Nir Ohad, Yudi Pawitan, and Trung Nghia Vu. 2021. “Circall: Fast and Accurate Methodology for Discovery of Circular RNAs from Paired-End RNA-Sequencing Data.” BMC Bioinformatics 22 (1): 495. https://doi.org/10.1186/s12859-021-04418-8.

datngu / Circall

readme

Circall: A fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data

Update news

11 July 2022: version 1.0.1

06 July 2022: version 1.0.0

19 June 2020: version 0.1.0

1. Introduction

Software requirements:

Annotation reference

2. Download and installation

3. Tutorial for human genome hg19 (GRCh37), annotation version 75.

3.1 Prepare BSJ reference database and Sqlite annotation file

Download genome fasta, transcript fasta and gtf annotation files.

Create sqlite

Create BSJ reference database

3.2 Indexing transcriptome and BSJ reference database

Index transcriptome

Index BSJ reference database

3.3 Run Circall pipeline

4. Tutorial for human genome hg38 (GRCh38), annotation version 106.

4.1 Prepare BSJ reference database and Sqlite annotation file

Download genome fasta, transcript fasta and gtf annotation files.

Create sqlite

Create BSJ reference database

4.2 Indexing transcriptome and BSJ reference database

Index transcriptome

Index BSJ reference database

4.3 Run Circall pipeline

5. Input, parameters, and output

Annotation data

Input data

Other parameters

Output

6. Circall simulator

Introduction

Parameter setting:

A toy example for using Circall simulator

7. License

8. Reference and citation