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caixu0518 / ITIPs

Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data
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How to detect the aligned and unaligned regions in step 2 ? #2

Closed Boer223 closed 2 years ago

Boer223 commented 2 years ago

Hi,

In Step 2, is there any scripts to detect the aligned and unaligned regions ?

caixu0518 commented 2 years ago

Sorry, i didnt include scripts in this step. here is my idea to do this.

The concepts were based on Chiifu-401 genomic sequences (reference genome). If genomic sequences from the other 19 accessions could be covered by the Chiifu-401 sequences, we denoted such regions as being ‘aligned regions’; if the genomic sequences in the other genomes could not be covered by the Chiifu-401 sequences, we defined them as ‘unaligned regions’.

Best. Xu

Boer223 commented 2 years ago

@caixu0518 Thank you! And is there any other tools to do that ? smartie-sv or minimap2 is OK?

caixu0518 commented 2 years ago

I used smartie-sv.

Boer223 commented 2 years ago

OK! Thank you!