Entering edit mode
2.2 years ago
PK
▴
130
Hi all,
I'm asking a question which is the following of my previous question (How to do the peak calling for introns?). One of the folks suggested me to do subset the intronic peaks from the output if i understood correctly. But i don't know how to do. What i have in my mind is that make my own gft file for specific subtypes of RNA (rRNA, miRNA, tRNA). And use that for mapping then do the peakcalling. Or is there any better way to do? What im trying to ask is that i have few i clip data to analysis. The problem is i have call the peaks for subtypes of RNA (Which i mentioned above).
What sort of environment or tools are you using? If you call peaks on the entire data set, can't you then take the peak locations and overlap them with feature locations to identify what features have peaks? You can do these sorts of queries on the command-line with things like bedtools, or in an environment like R with GenomicRanges, etc. More details might help.
Sure , Flexbar for trimming. STAR for mapping. MACS2/pirahna for peak calling. Also to extract features i use GenomicRanges/GenomicAlignments or ChIPpeakAnno. can't you then take the peak locations and overlap them with feature locations to identify what features have peaks? Can you suggest some tutorials. I'm kind of close by but not able to get. If you need more information just let me know