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LEARNING MATERIALS

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Code Block
languagebash
 $ git clone https://github.com/mcstitzer/maize_v4_TE_annotation.git
 $ cd maize_v4_TE_annotation/
 $ ls
helitron  line  ltr  README.md  sine  tir

 

Step 2: To predict structural LTRs

2.1 predict LTRs:

  • download tRNA and GyDb HMMs using get_tRNA_hmm_dbs.sh, which are needed forltrdigest

  • but LTR TEs are nested, so we need to remove these copies and rerun. This is done in mask_subtract

Code Block
languagebash
$ cd 

 

 

ltr
$ sh get_tRNA_hmm_dbs.sh 

This will download the tRNA database for all Eukaryotes

Code Block
languagebash
$ cd ltr
$ sh get_tRNA_hmm_dbs.sh