How to extract differential sequences between two genomes

[abcyulongwang]

Dear developer

Thank you for developing this software，I used the script “get_unmapped_pavs.pl” to extract the sequences on the unaligned reference genome in the BLASTN results and obtained the “genome_unmapped_pavs.txt” file with the following format:

“
chr1_100844159_100844261
chr1_102043848_102043985
chr1_1036133_1036273
chr1_103986404_103986566
chr1_105602622_105602721
chr1_105675100_105675279
chr1_107110623_107110795
chr1_109471225_109471352
chr1_111237450_111237564
chr1_111381914_111382097
chr1_11138775_11138960
chr1_11180499_11180669
”

If I want to get the unmapped sequence between the two genomes, I can extract the sequence in a specific interval on the chromosome, for example, extract the 100844159_100844261 position on chr1. Then, a collection of differential sequences between the two genomes is formed by merging with genome.absence.fa.

I want to know whether this approach is scientific and feasible, and I look forward to your reply.