Thanks for your pipeline! It's very exciting for RIC-seq data analysis.
But I have a question about annotation files in step3 category_intra_reads. I want to know how to get the exon_junction.bedpe file. Getting it from GTF file?
And another a question is that maybe some junction exons were not adjacent in the genome sequence(non-adjacent exon junction, that is, two exon sequences are not adjacent in the genome sequence but junction in the RNA sequence after alternative splicing). So how to identify these RNA ligation?
And one more question is that how to identify interaction between genes and non-annotated intergenic regions? Many regulatory elements, like a part of enhancers, are located at intergenic regions with inarticulate annotation. Because I think these interactions are neither interMolecular.withGene.sam (input in step5) nor intramolecular interactions (identified by step3 and step4).
Thanks again for your tools and look forward to your reply！
BIG zff
Thanks for your pipeline! It's very exciting for RIC-seq data analysis.
But I have a question about annotation files in step3 category_intra_reads. I want to know how to get the exon_junction.bedpe file. Getting it from GTF file?
And another a question is that maybe some junction exons were not adjacent in the genome sequence(non-adjacent exon junction, that is, two exon sequences are not adjacent in the genome sequence but junction in the RNA sequence after alternative splicing). So how to identify these RNA ligation?
And one more question is that how to identify interaction between genes and non-annotated intergenic regions? Many regulatory elements, like a part of enhancers, are located at intergenic regions with inarticulate annotation. Because I think these interactions are neither interMolecular.withGene.sam (input in step5) nor intramolecular interactions (identified by step3 and step4).
Thanks again for your tools and look forward to your reply！
BIG zff