Question: How do I tell piRNA population suppress TEs in a bed file?
0
gravatar for jaqx008
23 months ago by
jaqx00870
jaqx00870 wrote:

Hello everyone, I have two questions, 1. 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?

  1. How do I determine if I have a piRNA cluster? I will offer more clarity to my questions if it is'nt clear enough. Thanks in advance
ADD COMMENTlink written 23 months ago by jaqx00870

Quant information you have is for RNA but you are asking about inference for TE's which is an independent interval dataset?

ADD REPLYlink written 23 months ago by genomax85k

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.

ADD REPLYlink written 23 months ago by jaqx00870

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:

I want to know if the TEs are being repressed by the piRNAs and if yes, what percent?

Did you mean to ask if there is a TE present that piRNA is repressed?

Unless I am missing what you are asking completely.

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax85k

Exactly

Did you mean to ask if there is a TE present that piRNA is repressed?

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.

ADD REPLYlink written 23 months ago by jaqx00870

Check out bedtools intersect in that case. You will need to generate a BED format file for your piRNA locations so you can intersect that with TE. bedops also offers intersect operation.

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax85k

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.

ADD REPLYlink written 23 months ago by jaqx00870
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