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bioinfo-biols / CIRI-long

Circular RNA Identification for Nanopore Sequencing
https://ciri-cookbook.readthedocs.io
MIT License
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a minor bug for calculating circRNA sequence length #12

Closed JinwenBioinfo closed 2 years ago

JinwenBioinfo commented 2 years ago

Dear author, There may be a minor bug in your script that circRNA exon length has been shortened by one nt. e.g isoform exon structure : 1-100, 201-300 actual length: 200 yours: 198

My annotation is from GENCODE, which is 1-based format. The column circ_len of CIRI.info shows an incorrect value, an instance is as

circ_id logFC foldChange PValue pAdj diffState Chr_Start_End_Strand circBankID circbaseID mouse_circRNA_ID gene_id gene_name gene_type strand splice_site circ_type circ_len isoform
chr7:129813472-129815449 2.858076 7.250479 0.023715 0.042994 up chr7_129813472129815449- hsa_circTMEM209_032 hsa_circ_0082343 ENSG00000146842.12 TMEM209 protein_coding - AG-GT exon 308 129813472-129813569,129813665-129813779,129815352-129815449

Best wishes.

Kevinzjy commented 2 years ago

Hi @JinwenBioinfo , you're correct! We made a mistake when calculating the length from the isoform structure. I will fix it in the coming commit. Thanks for letting us know!