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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
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plot haplotype resolved genome by plotsr #8

Closed Chenglin20170390 closed 2 years ago

Chenglin20170390 commented 2 years ago

Hi Manish,

It's look nice for visualize the SV from different genomes.

However, In my case, I assembly several genomes with two haplotypes, I wondering whether I can use plotsr to show samples with two haplotype(different sample with different colour, each sample has two haplotype genomes with same colour).

Also, I can use plotsr to draw figure no more than 10 genomes. If more than 10 genomes, it will occur errors.

image

mnshgl0110 commented 2 years ago

Hi Lin,

whether I can use plotsr to show samples with two haplotype

Yes. In the genomes.txt file you can specify chromosome colours for individual genomes/haplotypyes. For example:

genome1_hap1.fasta  g1h1    lw:1.5;lc:red
genome1_hap2.fasta  g1h2    lw:1.5;lc:red
genome2_hap1.fasta  g2h1    lw:1.5;lc:blue
genome2_hap2.fasta  g2h2    lw:1.5;lc:blue

The issue with more than 10 genomes should be fixed in the newer versions. In case you are having issues in the latest version, then could you please open a new issue for that and also share the error message.

Best Manish

Chenglin20170390 commented 2 years ago

Hi Manish,

Many thanks for your quick reply !!!

This question is perfectly solved. I will open a new issue for plotsr with more than 10 genomes.

image

Thanks again.