Question: (Closed) How to classify TEs into the two TE classes?
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gravatar for jaqx008
9 months ago by
jaqx00840
jaqx00840 wrote:

Hello all. I have a Transposable element bed file. it contains a list TEs in the format below; I want to split this bed file into two seperate beds with one containing class I TEs and the other class II TEs. In my understanding, class I TEs are retroelements while class two TEs are DNA associated mobile elements. so what I did was filter out all the IDs with DNA and made that my class two bed. then the rest of the file were left as class I. I then used this for my downstream experiment to find small RNAs associated with this TEs. I am not sure if the way I seperated the TEs was right and I need help. Thanksin advance.

Bf_V2_1     19934   20000   +   CR1-45_BF           LINE/CR1       
Bf_V2_1     20796   20869   +   EnSpm-N1_BF         DNA/EnSpm      
Bf_V2_1     20954   21153   -   Jockey-1_BF         LINE/Jockey    
Bf_V2_1     21148   21206   -   bf_rep_30           Unknown        
Bf_V2_1     21577   22285   +   Harbinger-N3_BF     DNA/Harbinger
ADD COMMENTlink written 9 months ago by jaqx00840
1

This is more of a question on biology, i.e., on how to classify TEs. Please try another forum, like Biology StackExchange.

ADD REPLYlink written 8 months ago by Kevin Blighe42k

Hello jaqx008!

We believe that this post does not fit the main topic of this site.

Not related to bioinformatics

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 8 months ago by Kevin Blighe42k
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