How to classify TEs into the two TE classes?
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
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This is more of a question on biology, i.e., on how to classify TEs. Please try another forum, like Biology StackExchange.
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