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Alignment failed #24

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dinovski opened this issue Jan 10, 2023 · 0 comments
Open

Alignment failed #24

dinovski opened this issue Jan 10, 2023 · 0 comments

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@dinovski
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dinovski commented Jan 10, 2023 •
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I aligned an ONT generated FASTQ file to a reference fasta. The alignment completed with no error however no single read in the output SAM aligned to any region in the reference and all sam flags were equal to 255. There is no issue with the FASTQ or reference file as the alignment worked with minimap2.

Any advice would be appreciated.
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@dinovski