Inverted chromosome warning about syri HOT 5 CLOSED

@InfiniteLaugh You need to ensure that for homologous chromosomes same strands are present in the assembly files. You can check the dotplots (generated by fixchr) to decide whether the cleaned chromosomes corresponds to same strands. If you are confident that same strands are being compared, then you can ignore the warning.
If using the output of fixchr, you would need to realign the genomes generated by fixchr.

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@InfiniteLaugh You need to ensure that for homologous chromosomes same strands are present in the assembly files. You can check the dotplots (generated by fixchr) to decide whether the cleaned chromosomes corresponds to same strands. If you are confident that same strands are being compared, then you can ignore the warning. If using the output of fixchr, you would need to realign the genomes generated by fixchr.

Thank you for your immediate answer! ^_^
I looked through newly create file qry.filtered.fa & ref.filtered.fa , and found those warning Chromosome were successfully reversed by fixchr. As you have mentioned, if I try to use fixchr output to call SV, etc., do I have to run mummer again with new fasta files? Or just use the newly produced fasta file with original 108.THrd.coords file? Because I merely found any differences between homologous_strand_corrected_alignments.txt and the original 108.THrd.coords file produced by mummer.

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As you have mentioned, if I try to use fixchr output to call SV, etc., do I have to run mummer again with new fasta files?

Yes, you need to rerun alignments otherwise the genomes and alignments would not match.

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As you have mentioned, if I try to use fixchr output to call SV, etc., do I have to run mummer again with new fasta files?

Yes, you need to rerun alignments otherwise the genomes and alignments would not match.
Thanks for you rely. Now i am fully understand, it seems weird that so many technical posts shared online and published papers never mentioned this steps or issue before. LOL, maybe it's just a small tip for those experts.
In addition, may i open a new issue because i found SNPs output empty.

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Great that it is working. Please start a new issue for other questions.

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