Md Golam Rbbani

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”;"....

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...

Hello Jinyang, I have send you the gtf file. Please check your email. Thanks Rabbani

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 '#' .

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 '#' .

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 '#' .

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.

Hello Jinyang, Reference GTF looks fine. it has "gene_id" attribute