Activity for CIRI
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CIRI released /CIRI-full/CIRI_Full_v2.1.1.jar
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Jinyang Zhang posted a comment on discussion General Discussion
Hi Chee How, CIRI-full doesn't support trimmed reads with variable sequence length, please use raw reads instead. -Jinyang
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Chee How Teo posted a comment on discussion General Discussion
Dear author of CIRI-FULL, Good day! I am trying to use CIRI-FULL.jar for my circRNA analysis. I am facing problem with CIRI-FULL.jar Pipeline when I used the clean reads trimmed by cutadapt versionh 1.9.1 for CIRI-FULL analysis. The detail of the problem is given here: java -jar CIRI-full.jar Pipeline -1 Be96hpi-3-LDB10460_clean_L2_1.fq.gz -2 Be96hpi-3-LDB10460_clean_L2_2.fq.gz' -r reference.fna -a reference.gtf -t 8 -0 -o Be96hpi-3 -d Be96hpi-3 classpath = /home/umcentral18/Downloads/CIRI-full_v2_1//...
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Mohammad created ticket #15
In all my dataset samples I have no detect any Circular RNA
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Hi Dario, I think the overlapping reads in your libraries are causing the problem. These overlapping BSJ reads will have distinct alignment pattern than normal paired-end reads, and thus could be filtered out as false positive. Have you tried using reads merging tools (e.g. FLASH) to merge overlapping short reads, and run CIRI2 on merged and unmerged reads respectively, then use the sum of BSJ reads in two parts of reads as final results? I think this could be a convenient solution.
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Dario created ticket #14
CIRI2 not working properly with overlapping paired-end reads
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Rodrigo Silva Araujo Streit created ticket #13
Issues with test_CIRI.pl
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pc created ticket #12
CIRI-vis/full not giving full output
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Hao'zhang posted a comment on ticket #1
Following the suggestion by the author, I will try to use raw reads instead of trimmed reads.
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I meet the same problem because my data have been trimmed by fastp.
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Yuan Gao posted a comment on ticket #11
Hi Kandarp, We never met that situation before. Did you use parallel Perl 5.8 or higher? Could you please also let me see the lines around line 280,269 of the sam file that you input? Thanks, Yuan
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Kandarp Joshi created ticket #11
CIRI2 test and program fails
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split in CIRI2 fails on large datasets (output suffixes exhausted)
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Redirect BWA-mem sam file to CIRI 2.0.6
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Error running CIRI with gff files
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CIRI's coding
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kill process when I want to scan sample for second time via running CIRI2
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circRNA quantification
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CIRI not progressing past second scan
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Error in running CIRI2
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As we mentioned in our paper and manual, CIRI is a de novo detection tool, which does not depend on annotation for detecting loci of circRNAs on reference genome and can be used for non-model organisms without complete annotation. The annotation can be used for output of gene ID for detected circRNAs or as a complementary filtration in addition to GT-AG splicing signals, but the detected circRNAs are almost the same whether annotation is provided or not.
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Md Golam Rbbani posted a comment on ticket #5
Dear Yuan, I want to ask you one more question. If i run ciri without gtf i win not have information of circular rna type and gene id but will it predict circular rna correctly? Thanks Rabbani On Thu, Aug 29, 2019 at 11:20 PM Yuan Gao gy-james@users.sourceforge.net wrote: Hi Golam, I think I know what the problem is. There are 420 lines in your GTF which do not have the key words “gene_id”. For example, "NC_035898.1 Gnomon exon 10221156 10221698 . - . transcript_id "id17563"; gene_name "LOC111194270”;"....
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Hi Golam, I think I know what the problem is. There are 420 lines in your GTF which do not have the key words “gene_id”. For example, "NC_035898.1 Gnomon exon 10221156 10221698 . - . transcript_id "id17563"; gene_name "LOC111194270”;". Please remove or modify these lines so that CIRI2 can run successfully. Thanks, Yuan
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Could you please send the first 100 lines of GTF file to me too (gy.james@163.com)? Thanks.
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Could you please sent the first 100 line of GTF file to me too (gy.james@163.com)? Thanks.
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Hi Yuan gao, CIRI2 cannot understand reference.gtf. at CIRI.pl line 319, <anno> line 1.</anno> This is the error message i have got in error long. According to Jinyang Zhang's suggestion, i am using without GTF and it is working fine. Could you please clarify it for me? Thanks, *Rabbani * On Thu, Aug 29, 2019 at 6:55 PM Yuan Gao gy-james@users.sourceforge.net wrote: If you got the error message from line 319, that is due to the reference file cannot be found or read. I believe the error message is...
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If you got the error message from line 319, that is due to the reference file (FASTA) cannot be found or read. I believe the error message is like "Reference file is not readable".
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If you got the error message from line 319, that is due to the reference file cannot be found or read. I believe the error message is like "Reference file is not readable".
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Hello Jinyang, I have send you the gtf file. Please check your email. Thanks Rabbani
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Hi Rabbani, Sorry for the inconvenience. Could you send the GTF file or first 100 lines of it to my email zhangjinyang@biols.ac.cn ? I will check why CIRI2 failed to load your annotation file. Thanks, Jinyang
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Hello JinYang, I have tried V2.0.6 , v2.0.5 and v2.0.5. ALL of the virsion have same error message. HOwever, with CIRI1 it was fine. since i need strand info, i want to use CIRI2. N.B : I have checked my GTF file and there is no header sequence that starts with '#' .
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Hello JinYang, I have tried V2.0.6 and v2.0.5. both of the virsion have same result. HOwever, with CIRI1 it was fine. since i need strand info, i want to use CIRI2. N.B : I have checked my GTF file and there is no header sequence that starts with '#' .
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Hello JinYang, I have tried V2.0.6 and v2.0.5. both of the virsion have same result. HOwever, with CIRI1 it was fine. since i need strand info, i want to use CIRI2. N.B : I have checked my GTF and there is no header sequence that starts '#' .
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Hello JinYang, I have tried V2.0.6 and v2.0.5. both of the virsion have same result. HOwever, with CIRI1 it was fine. since i need strand info, i want to use CIRI2.
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Hi Rabbani, I am not sure what cause the problem. If the first few lines of your GTF file contain header information start with '#', you can remove them and try again. P.S. Are you using the latest version (v2.0.6) of CIRI2? It seems that the error message is generated from an obsolute version. Thanks, Jinyang
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Hello Jinyang, Reference GTF looks fine. it has "gene_id" attribute
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Hello Jinyang, Reference GTF looks fine. it has "gene_id" attribute
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Hi Rabbani, Please check the attribute column (column 9) in your reference.gtf. CIRI2 need the "gene_id" attribute for circRNA annotation. If your annotation file do not provide this information, you need to run CIRI2 without it.
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Hi Rabbani, Please the attribute column (column 9) in your reference.gtf. CIRI2 need the "gene_id" attribute for circRNA annotation. If your annotation file do not provide this information, you need to run CIRI2 without it.
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Hi Mohammad, Please the attribute column (column 9) in your reference.gtf. CIRI2 need the "gene_id" attribute for circRNA annotation. If your annotation file do not provide this information, you need to run CIRI2 without it.
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Hi Yuan, I am using CIRI2 to analyse my data set using Perl CIRI2 -I in.sam -O out.ciri -F reference.fa -A reference.gtf -T 4 command but getting error message CIRI2 cannot understand reference.gtf. at CIRI.pl line 319, <anno> line 1.</anno> DO i need to run without .gtf file in CIRI2?? Thanks Rabbani
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CRISTIAN PADRON modified a comment on discussion General Discussion
I was trying to use the test data that is provided by CIRI-full for running the program I did well in every step but when is the time to use CIRI-vis.jar, in linux and OS found the same error: cBook-Air-de-Cristian-9:CIRI-full_v2.0 CristianPadron$ java -jar CIRI-vis.jar Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2D at java.base/java.lang.Class.forName0(Native Method) at java.base/java.lang.Class.forName(Class.java:398) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:56)...
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I was trying to use the test data that is provided by CIRI-full for running the program I did do well in every step but when is the time to use CIRI-vis.jar, in linux and OS found the same error: cBook-Air-de-Cristian-9:CIRI-full_v2.0 CristianPadron$ java -jar CIRI-vis.jar Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2D at java.base/java.lang.Class.forName0(Native Method) at java.base/java.lang.Class.forName(Class.java:398) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:56)...
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I was trying to use the test data that is provided by CIRI-full for running the program I did do well in every step but when is the time to come to use CIRI-vis.jar, in linux and OS found the same error: cBook-Air-de-Cristian-9:CIRI-full_v2.0 CristianPadron$ java -jar CIRI-vis.jar Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2D at java.base/java.lang.Class.forName0(Native Method) at java.base/java.lang.Class.forName(Class.java:398) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:56)...
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CIRI v1.2 needs more time and memory. Please use latest version v2.0.6 for your analysis. If the results will be further used for CIRI-AS, please make sure the read length is the same.
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Lachlan G Gray created ticket #10
CIRI not progressing past second scan
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I have forwarded the ticket to the author of CIRI-full, Yi.
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Marc M. Wellman posted a comment on discussion General Discussion
In the last file (merge_circRNA_detail.anno) I cannot see a column to get the number of reads that have been aligned to each circRNA. There are other files (like splice.list) that do have this information, but the number of circRNAs is different, and not even a single coordinate match between files (I would say it is because the coordinates in the splice.list refer to the coordinates where the splice occur but not in the merge file).
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circRNA quantification
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Shrey Gandhi modified a comment on ticket #1
I also face the same issue.. Did anyone find the solution to this problem?
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I also face the same issue.. Did anyone find the problem?
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Worked perfectly! Thanks :-)
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kill process when I want to scan sample for second time via running CIRI2
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Hi Johann, CIRI not only adds details of gene ID according to the annotation provided, but can also use exon ends in annotation to search potential circRNAs with no GT-AG splicing signals. So usually more circRNAs are found when annotation is provided. Thanks, Yuan
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Johann created ticket #7
CIRI's coding
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Hi Yuan Thanks Mohammad
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Hi Mohammad, Please download test_data2.zip contained in the CIRI2 folder to test CIRI2. Thanks, Yuan
