I am currently working on the implementation of a little package on R which seeks to make predicting operons from RNA-seq data with paired-end reads. Now, I'm looking for a package on R or a tool like Bedtools to do this :
I have two annotation files, one in GTF the other in GFF3 format (with the name of the genes and their coordinates etc ...) And a file in BED format which contains the reads (in paired-end) that I can sort by position or by read pair. I want to find all the genes that are overlapped by one fragment (read1 + read2 reassembled) based on their genomic coordinates. Or better yet, pairs of different genes that are overlapped by one fragment.
I read a lot of fonction that seems to do this but I'm not very sure of the result and I don't know which is the best between Bedtools intersect, annotate etc ... Or GenomicRange, findOverlap on R etc ...
If someone have a suggestion, I'll take it.