I am running
CIRIquant on Ubuntu 16.04 LTS following the instruction which indicated on https://ciriquant-cookbook.readthedocs.io/en/latest/de.html. I got .GTF file that contains detailed information of BSJ and FSJ reads of circRNAs and annotation of circRNA back-spliced regions.
In the following, I added a record of Circular RNA detected in .GTF file:
Chrom: chr1 Type: circRNA start: 1289228 End: 1289448 score:0.02 Strand Information: - circ_id: chr1:1289228|1289448 circ_type :exon bsj: 1000 fsj: 515.000 junc_ratio: 0.004 gene_id: ENSG00000162576.12 gene_name: MXRA8 gene_type: protein_coding
I need to know which column of .GTF file indicates the expression count of circular detected?
I appreciate it if you share your comment with me.