Open theo-allnutt-bioinformatics opened 1 year ago
Hi,
using a test file of three chloroplast genomes, attached, minimap2 fails to properly align all repeats - the inverted repeat of the genomes are not shown - see plots below.
brassica_chloroplast.fasta.txt
minimap2 -x asm20 -t 48 brassica_chloroplast.fasta brassica_chloroplast.fasta > brassica.paf pafCoordsDotPlotly.R -i brassica.paf -o brassica -q 100 -m 100 -p 8 -l -x -k 3
but nucmer method looks ok: nucmer --maxmatch -l 80 -c 100 brassica_chloroplast.fasta brassica_chloroplast.fasta -p brassica.nucmer mummerCoordsDotPlotly.R -i brassica.delta.coords -o brassica.plot -x -m 100 -q 100 -k 3 -s -t -l -p 12
I am not sure if this is problem with dotPlotly or minimap2, but it does mean that quite large alignments are missed.
Thanks,
Theo
Hi,
using a test file of three chloroplast genomes, attached, minimap2 fails to properly align all repeats - the inverted repeat of the genomes are not shown - see plots below.
brassica_chloroplast.fasta.txt
minimap2 -x asm20 -t 48 brassica_chloroplast.fasta brassica_chloroplast.fasta > brassica.paf pafCoordsDotPlotly.R -i brassica.paf -o brassica -q 100 -m 100 -p 8 -l -x -k 3![image](https://user-images.githubusercontent.com/37783866/212792671-18dc95e3-3fba-461c-8dc9-ed0528cd8ff9.png)
but nucmer method looks ok: nucmer --maxmatch -l 80 -c 100 brassica_chloroplast.fasta brassica_chloroplast.fasta -p brassica.nucmer mummerCoordsDotPlotly.R -i brassica.delta.coords -o brassica.plot -x -m 100 -q 100 -k 3 -s -t -l -p 12![image](https://user-images.githubusercontent.com/37783866/212792784-d8e00f9b-2a83-4ab0-bafc-ee1fab444088.png)
I am not sure if this is problem with dotPlotly or minimap2, but it does mean that quite large alignments are missed.
Thanks,
Theo