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IGV not finding sequence from bam file generated from a graphmap2 sam file #25

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Coahuila opened this issue Apr 6, 2023 · 0 comments

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@Coahuila
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Coahuila commented Apr 6, 2023

Hi,
I have Oxford Nanopore DNA sequences (from Plasmidsaurus) that I'm generating sam files through graphmap2, and ultimately making sorted bam files. However, the bam files show no sequence when I load them into IGV. The reference fasta is only 700bp long. My guess you could look at an output sam file and tell me the issue, but I can send you whatever files would help. I would appreciate any kind of direction you might give.

Thanks,

Patrick

Example_part.sam.txt

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