Sorry if this question has been addressed elsewhere but I couldn't find it.
I have used my ONT genomic reads to identify SVs in my sample genome. While deletions are kind of easy to handle as they can be easily excluded from the analysis I was wondering if there is a way to quantify methylation in newly identified insertions. Currently modkit pileup takes a reference fasta so while this information is in the input bam file it is not extracted into bedmethyl since these regions don't have a coordinate in the reference genome. I am currently trying to build a custom genome, but is there a simpler way to use modkit pileup in the insertions? I have the insertion coordinate and their length from the SV identifier I used if that is helpful. I can also extract their sequences into a fasta.
Please let me know if this is possible without having to build a new genome.
Thank you for your help.
Mafalda
Sorry if this question has been addressed elsewhere but I couldn't find it.
I have used my ONT genomic reads to identify SVs in my sample genome. While deletions are kind of easy to handle as they can be easily excluded from the analysis I was wondering if there is a way to quantify methylation in newly identified insertions. Currently modkit pileup takes a reference fasta so while this information is in the input bam file it is not extracted into bedmethyl since these regions don't have a coordinate in the reference genome. I am currently trying to build a custom genome, but is there a simpler way to use modkit pileup in the insertions? I have the insertion coordinate and their length from the SV identifier I used if that is helpful. I can also extract their sequences into a fasta.
Please let me know if this is possible without having to build a new genome.
Thank you for your help.
Mafalda