Page Comparison

...

 $ 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

$ cd ltr
$ sh get_tRNA_hmm_dbs.sh 

...

This will download the tRNA database for all Eukaryotes

• run_ltrharvest.sh runs ltrharvest and ltrdigest on the genome

$ cd ltr
$ sh get_tRNA_hmm_dbs.sh