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nanoporetech / dorado

Oxford Nanopore's Basecaller
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Dorado basecalling what's next ? Correlation with modkit output and transposable elements #810

Closed OceaneMion closed 1 month ago

OceaneMion commented 1 month ago

Hi all, I have performed dorado modified basecalling on my data, obtain my assemblies and performed a modkit pileup on them to have my methylation data.

I have filtered my data to have output as follow : contig_102 0 1 0 contig_102 1 2 0 contig_102 2 3 0 contig_102 3 4 0 contig_102 4 5 0 contig_102 5 6 0 contig_102 6 7 0 contig_102 7 8 0 contig_102 8 9 0 contig_102 9 10 3.45

With the first column being the contig name, the second the start position, the third the ending position, and the last column the methylation probability

I have also perform RepeatModeler and RepeatMasker step to annotate my transposable element, and filtered my data to obtain output as follow : contig_102 10317 10662 LTR contig_102 10664 11011 LTR contig_102 36398 36453 LTR contig_102 39665 39748 LTR contig_102 40983 41101 LTR/Gypsy

My question is do you have any code/pipeline on how to obtain a plot similar to this : image

I know that I can kinda use bedtools intersect to obtain the methylation marks in my transposable elements Any help will be appreciate, thanks in advance.

HalfPhoton commented 1 month ago

Hi @OceaneMion, Respectfully this is not a dorado issue and as such I'm closing it. Please seek assistance in a bioinformatics forum where they're likely able to help you.

Kind regards, Rich

OceaneMion commented 1 month ago

Thanks for your anwser I will see with the creator of modkit as it is more correlated with their work.

Le mer. 15 mai 2024 à 18:42, Richard Harris @.***> a écrit :

Hi @OceaneMion https://github.com/OceaneMion, Respectfully this is not a dorado issue and as such I'm closing it. Please seek assistance in a bioinformatics forum where they're likely able to help you.

Kind regards, Rich

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