About¶
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).
Release Notes¶
Version 1.4
Installation¶
Prerequisites¶
Softwares:
JavaSE >= 1.6
bwa
CIRI2
CIRI-AS
CIRI-Full
Install CIRI-vis¶
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.
Commands and Arguments¶
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
...
Output files¶
Description of prefix.list
:
This file gives the detailed information of circRNA isoforms. Columns are separated by tabs:
Columns | Description |
---|---|
Image_ID | The name of pdf file. |
Circle_ID | ID of the BSJ position of circRNA isoform in the pattern of "chr:start |
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
Columns | Description |
---|---|
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 |
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)
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