Some question about TIPs indentifacation in population scale

[Axolotl233]

Hi,

Recently i read the paper: "Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa", thats amazing works and very interesting for me, because i want apply this method in my project.

I have one genome assembly with TE annotation files and some illumina paired reads of several population, i want to know if i can skip step1 and step2, just manually extract <ref.referenceTEinsertions_and_flanking1kb.fasta> as input of step3 or there have other way to get correct input file.

Anyway, if ITIPs could not compatiable for our data, could you recommend a few softwares that work with my data?

Thanks,
Wenjie

[Axolotl233]

Hi, is there any process?

[caixu0518]

Yes，you can use your customized fasta format file as the input. Just note that the length of the flank sequence is 1 kb