Hi,
I have 11 chromosomes in both my reference and query sequences. However, after using Minimap2 to generate a PAF file and then using pafCoordsDotPlotly.R to plot it, the y-axis displays 11 chromosome IDs while the x-axis only displays 9 chromosome IDs. I am sure that my reference sequence contains all 11 chromosomes. I do not know why two chromosome ID numbers are missing on the x-axis.
There are my command line：
/minimap2 -x asm5 $ref $query -t $thread > $out_dir/"$prefix".minimap2.paf
pafCoordsDotPlotly.R -i "$prefix".minimap2.paf -o "$prefix".drplot -k 11 -q 10000 -m 200000 -r chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11 -x
Log file prompt：
PARAMETERS:
input (-i): cpxp.minimap2.paf
output (-o): cpxp-x.drplot
minimum query aggregate alignment length (-q): 10000
minimum alignment length (-m): 2e+05
plot size (-p): 15
show horizontal lines (-l): FALSE
number of reference chromosomes to keep (-k): 11
show % identity (-s): FALSE
show % identity for on-target alignments only (-t): FALSE
produce interactive plot (-x): FALSE
reference IDs to keep (-r): chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11
Number of alignments: 107168
Number of query sequences: 11
After filtering... Number of alignments: 1596
After filtering... Number of query sequences: 11
Warning: ‘timedatectl’ indicates the non-existent timezone name ‘n/a’
Warning: Your system is mis-configured: ‘/etc/localtime’ is not a symlink
Warning: It is strongly recommended to set envionment variable TZ to ‘Asia/Chongqing’ (or equivalent)
Looking forward to your reply
Thanks.
Lyu Qiang
Hi,
I have 11 chromosomes in both my reference and query sequences. However, after using Minimap2 to generate a PAF file and then using pafCoordsDotPlotly.R to plot it, the y-axis displays 11 chromosome IDs while the x-axis only displays 9 chromosome IDs. I am sure that my reference sequence contains all 11 chromosomes. I do not know why two chromosome ID numbers are missing on the x-axis.
There are my command line：
/minimap2 -x asm5 $ref $query -t $thread > $out_dir/"$prefix".minimap2.paf
pafCoordsDotPlotly.R -i "$prefix".minimap2.paf -o "$prefix".drplot -k 11 -q 10000 -m 200000 -r chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11 -x
Log file prompt：
PARAMETERS:
input (-i): cpxp.minimap2.paf
output (-o): cpxp-x.drplot
minimum query aggregate alignment length (-q): 10000
minimum alignment length (-m): 2e+05
plot size (-p): 15
show horizontal lines (-l): FALSE
number of reference chromosomes to keep (-k): 11
show % identity (-s): FALSE
show % identity for on-target alignments only (-t): FALSE
produce interactive plot (-x): FALSE
reference IDs to keep (-r): chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11
Number of alignments: 107168
Number of query sequences: 11
After filtering... Number of alignments: 1596
After filtering... Number of query sequences: 11
Warning: ‘timedatectl’ indicates the non-existent timezone name ‘n/a’
Warning: Your system is mis-configured: ‘/etc/localtime’ is not a symlink
Warning: It is strongly recommended to set envionment variable TZ to ‘Asia/Chongqing’ (or equivalent)
Looking forward to your reply
Thanks.
Lyu Qiang