Identify Duplication

[wyim-pgl]

Hi, I have been testing Anchorwave, to check the genome duplication. It didn't give me expected result with -R 1 -Q 3. I checked MAF and converted MAF to many other format but I couldn't find any 1:3 match in the result. Can you share some idea?

anchorwave gff2seq -r Athaliana_167_TAIR9.fa -i Athaliana_167_TAIR10.gene.gff3  -o cds.fa

minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 Athaliana_167_TAIR9.fa cds.fa > ref.sam
minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 Saharan.fasta cds.fa > cds.sam

anchorwave proali -i Athaliana_167_TAIR10.gene.gff3 -r Athaliana_167_TAIR9.fa -as cds.fa   -a cds.sam -ar ref.sam -s Saharan.fasta -n anchors -R 1 -Q 3 -o alignment.maf -f alignment.f.maf -t 4

[baoxingsong]

Thanks for your feedback. AnchorWave has not been developed to check genome duplication. You should know the whole genome duplications before running AnchorWave. If you expect Saharan has a triplication, you should set "-R 3 -Q 1".

[wyim-pgl]

Hi @baoxingsong, We already knew that the Saharan has triplication. I will run it with -R 3 -Q 1 and give you update. By the way, can we use Saharan -R3 -Q3 itself?