Entering edit mode
5.7 years ago
jaqx008
▴
110
Hello everyone, I have two questions,
- I have an RNA seq data from which I generated piRNA and siRNA files. I also have Transposable element bed file. I want to know if the TEs are being repressed by the piRNAs and if yes, what percent?
- How do I determine if I have a piRNA cluster? I will offer more clarity to my questions if it isn't clear enough.
Thanks in advance
Quant information you have is for RNA but you are asking about inference for TE's which is an independent interval dataset?
Not sure what you are asking, But I have piRNAs made from RNAseq and mapped it to the refernece genome and now have piRNasorted.bam files. Now Im trying to see if the piRNAs repress the TEs but dont know how.
What I was asking is how are you going to relate those two. You can only overlap the intervals for TE (transposable elements or something else?) with the piRNA but how are you going to conclude this:
Did you mean to ask if there is a TE present that piRNA is repressed?
Unless I am missing what you are asking completely.
Exactly
THats what I'm trying to ask. Sorry for not putting it right. However, TE bed file was made from the genome and the piRNA from RNA seq was mapped to the genome, so there should be overlap between the piRNA and TEs I assume.
Check out
bedtools intersectin that case. You will need to generate a BED format file for your piRNA locations so you can intersect that with TE.bedopsalso offersintersectoperation.This did help and it pulled out the loci cordinates. Might you have an idea how I can tell if the piRNAs are clustered? as in my second question.