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Issues about FAST-iCLIP pipeline #35

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Zzy190516 opened this issue Dec 24, 2024 · 0 comments
Open

Issues about FAST-iCLIP pipeline #35

Zzy190516 opened this issue Dec 24, 2024 · 0 comments

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@Zzy190516
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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.
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