Issues about FAST-iCLIP pipeline

[Zzy190516]

Excuse me, I have 2 questions about the code and pipieline of calculating expression counts in FAST-iCLIP:

1. Bedtools is employed for counting RNA expression based on code. And I also saw that there was a folder named docs, including some gene and RNA position files. However, how should I deal with the gene (or snoRNA) regions that have overlap regions? For the reads mapped to these regions, they will be calculated more than once based on the code.
2. I found that some gene (or snoRNA) regions are very close. At this condition, how should I deal with the reads, which mapped to 2 near gene (or snoRNA) regions at same time? I don't think that counting them more than once is suitable.