Hi Cao,
Really impressive work — thanks for sharing the RIC-seq pipeline!
I have downloaded the raw RIC-seq fastq files and successfully finished the first part of the pipeline (1.find_pairTags_from_STAR_results). Now I have obtained the final interaction.sam files for each sample.
I’d like to visualize the genome-wide RNA–RNA interactions, similar to what was shown in your paper. Could you please let me know:
How can I generate a whole-genome .hic file for visualization in Juicebox?
Or alternatively, how can I create the arc-style .bed file for visualization in IGV?
I noticed that the script in 2.construct_hicFiles_for_rRNA seems mainly designed for rRNA interactions. Should I modify it or use another module for mRNA-genome-wide interactions?
Thank you very much for your time and guidance!
Hi Cao,
Really impressive work — thanks for sharing the RIC-seq pipeline!
I have downloaded the raw RIC-seq fastq files and successfully finished the first part of the pipeline (1.find_pairTags_from_STAR_results). Now I have obtained the final interaction.sam files for each sample.
I’d like to visualize the genome-wide RNA–RNA interactions, similar to what was shown in your paper. Could you please let me know:
How can I generate a whole-genome .hic file for visualization in Juicebox?
Or alternatively, how can I create the arc-style .bed file for visualization in IGV?
I noticed that the script in 2.construct_hicFiles_for_rRNA seems mainly designed for rRNA interactions. Should I modify it or use another module for mRNA-genome-wide interactions?
Thank you very much for your time and guidance!