Can I run xTEA for mice genomes? & how can i do it?

[sahuno]

No description provided.

[simoncchu]

The current released repeat library only works for human, not mice genome. To work on mice, you have to build a mice specific library. This thread may help: #20

[sahuno]

Hi, reading the instructions
how can i generate TE-type.consensus.fa ?
2. for mouse mm10 would this mm10.fa.out.gz be the TE-type_rmsk.out ? for which i'll extract only LINE1 by
grep "LINE1" mm10.fa.out.gz > mm10_L1.out

[simoncchu]

You can check whether you can find the consensus of the specific subfamily (the active L1 in the species you are checking) from RepBase. Or you can generate by yourself.

For the repeatmasker file, yes that's the file, but you should parse out the active mouse L1 subfamilies, not all the "LINE1"