CIRI Files

CIRI-vis

CIRI-vis is a tool for visualizing alignments of BSJ & RO merged reads and estimating the related abundance of isoforms according to the output of CIRI-full (prefix_merge_circRNA_detail.anno) or CIRI-AS (prefix_jav.list).

Author

Authors: Yi Zheng(zhengyi@biols.ac.cn), Fangqing Zhao(zhfq@biols.ac.cn)

Maintainer: Yi Zheng

Release Notes

• Version 1.4

Prerequisites

Softwares:
    JavaSE >= 1.6
    bwa
    CIRI2
    CIRI-AS
    CIRI-Full

1. Installation

CIRI-vis is developed in JAVA, and it can be performed in any system which has Java SE Runtime Environment.

CIRI-vis is already packed with the CIRI-full software under /bin. After downloading the CIRI-full package, you can extract it by typing:

unzip CIRI-full_v2.0.zip

you can find CIRI-vis.jar in the folder.

2. Running CIRI-vis

Input file requirements:

IF you runned CIRI-full Pipeline in previous step, the input file will be named:XXX_merge_circRNA_detail.anno under CIRI-full_output folder

IF you only run CIRI-AS with '-d yes' parameter in previous step, the input file will be named XXX_jav.list under your CIRI-AS output folder

Library length file is nessaracy for isoform expression estimation. library length file will be XXX_library_length.list under your CIRI-AS output folder

CIRI-vis.jar runs from a command line as follows:

Usage: java -jar CIRI-vis.jar [Options]

Options:

-i          The path of input file of CIRI-vis. (required)
-l          The path of library length file. (required for isoform quantification)
-r          The path of reference genome sequence in FASTA format. (required for output circRNA sequence)
-list       The list of choosen circRNA BSJ.(It is needed when more than one sample)
-d          The dictionary of output. Default currentdir/stdir
-o          The prefix of output. Default stout (optional)
-type       The format of figure. you can select pdf or svg or both. Default pdf (optional)
-max        The maximum expression (BSJ reads number) of circRNA that displayed by CIRI-vis. Default 999999999 (optional)
-min        The minimum expression (BSJ reads number) of circRNA that displayed by CIRI-vis. Default 5. Note: please only use one of -min, -exp, -rank (optional)
-rank       Only display the expression top X% of circRNA (optional)
-exp        Only display the top expression circRNA that contain X% of BSJ reads. (optional)
-iso        The maximum number of considering isoform, default 10. High value will make the quantification slower (optional)
-ran        Set random seed, default 0.(optional)

Examples:

For one sample

java -jar CIRI-vis.jar -i A_merge_circRNA_detail.anno -l A_library_length.list -r Ref.fa -d out -o prefix

For more than one samples

java -jar CIRI-vis.jar -i A_merge_circRNA_detail.anno B_merge_circRNA_detail.anno -l A_library_length.list B_library_length.list -r Ref.fa -d out -o prefix -list test.txt

The format of the "test.txt" (input of -list) should be:

chr10:74474869|74475660
chr8:141856359|141900868    
...

3. Output files

Description of prefix.list:

This file gives the detailed information of circRNA isoforms. Columns are separated by tabs:

Image_ID:       The name of pdf file.
Circle_ID:      ID of the BSJ position of circRNA isoform in the pattern of "chr:start|end";
Chr:            chromosome of a predicted circRNA isoform
start:          start loci of a predicted circRNA isoform on the chromosome
end:            end loci of a predicted circRNA isoform on the chromosome
total_exp:      circular junction read (also called as back-spliced junction read) count of a predicted circRNA
isoform_number: the serial number of isoform in circRNA
isoform_exp:    the estimate BSJ read count of this predicted isoform.
isoform_length: the minimum length of this predicted isoform.
isoform_state:  whether this predicted isoform is fully reconstructed.
strain:         strain of circRNA (+/-)
gene_id:        gene name that the circRNA located in
isoform_cirexon: The cirexon position in this predicted isoform, "0-0" represent for the breakpoint during reconstruction.

When more than one sample

Image_ID:       The name of pdf file.
Sample_name:     Name of input sample (appear only when more than one sample)
Circle_ID:      ID of the BSJ position of circRNA isoform in the pattern of "chr:start|end";    
Chr:            chromosome of a predicted circRNA isoform
start:          start loci of a predicted circRNA isoform on the chromosome
end:            end loci of a predicted circRNA isoform on the chromosome
total_exp:      circular junction read (also called as back-spliced junction read) count of a predicted circRNA
isoform_number: the serial number of isoform in circRNA
isoform_exp:    the estimate BSJ read count of this predicted isoform.
isoform_length: the minimum length of this predicted isoform.
estimated_isoform_read_count:   The estimated total number of read that on this isoform (including BSJ and nonBSJ reads),
isoform_state:  whether this predicted isoform is fully reconstructed.
strain:         strain of circRNA (+/-)
gene_id:        gene name that the circRNA located in
isoform_cirexon: The cirexon position in this predicted isoform, "0-0" represent for the breakpoint during reconstruction.

Description of prefix.fa:

This FASTA format file will be generated if reference genome sequence is available. It contains the sequence of fully reconstructed isoform. They were named in this format:

>(Image_name)#(BSJ) length=(isoform_length) (isoform_BSJ_read_count)/(circRNA_BSJ_read_count)

4. Example Usage

Test data sets (FASTQ file, annotation file and reference sequence) are packaged with the CIRI-full software, which can be found in the CIRI-full_test/ folder. Temporary and final results are given in the CIRI-full/test_output/ folder. Here are the commands for running the test data sets:

cd CIRI-full_v2.0/CIRI-full_test/
bwa index test_ref.fa
java -jar ../CIRI-full.jar Pipeline -1 test_1.fq.gz -2 test_2.fq.gz -a test_anno.gtf -r test_ref.fa -d test_output/ -o test
unset DISPLAY
java -jar CIRI-vis.jar -i test_output/CIRI-full_output/test_merge_circRNA_detail.anno -l ../CIRI-vis_test/test_library_length.list -r test_ref.fa -d test_output/CIRI-vis_out -min 1