Hello! I am having problems with generating my QTLplot.
I have run QTLseq for my sequences and the initial QTLplot from this run has does not have a smooth red line. So I decided to run QTLplot using the vcf file from my QTLseq run using the code below:
qtlplot -v qtlseq.vcf.gz \
-o bsa_plot \
-n1 10 \
-n2 10 \
-w 2000 \
-s 100
Here’s the picture:
I tried changing the -w to 1000 and the chromosomes are okay. But running the same -w 1000 for the second time, chromosomes 1-5 are lost (picture below). Same with when I run -w 3000, first one is okay and the rerun has missing chromosomes.
-w 1000 rerun
-w 3000 rerun
I don't understand why. Hope you could help. Thank you very much! :)
Hello! I am having problems with generating my QTLplot. I have run QTLseq for my sequences and the initial QTLplot from this run has does not have a smooth red line. So I decided to run QTLplot using the vcf file from my QTLseq run using the code below: qtlplot -v qtlseq.vcf.gz \ -o bsa_plot \ -n1 10 \ -n2 10 \ -w 2000 \ -s 100
Here’s the picture:
I tried changing the -w to 1000 and the chromosomes are okay. But running the same -w 1000 for the second time, chromosomes 1-5 are lost (picture below). Same with when I run -w 3000, first one is okay and the rerun has missing chromosomes.
-w 1000 rerun
-w 3000 rerun
I don't understand why. Hope you could help. Thank you very much! :)