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pedronachtigall / MITGARD

Mitochondrial Genome Assembly
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There is N in the assembly result, and the downstream cannot be annotated. How to solve it? #6

Open deyuanyang opened 7 months ago

deyuanyang commented 7 months ago

Hi,

When appear N character in the results, I can not use these sequences to annotation, how to solve it?

pedronachtigall commented 6 months ago

Hi @deyuanyang ,

Thank you for using MITGARD in your analysis. It is important to notice that the N's means that your dataset does not have sufficient coverage for that region. This is a common issue in RNA-seq data when there is not enough sequencing depth.

The annotation is not performed by MITGARD. We just give some pieces of advice on how to perform annotations using MITOS2 or MitoZ. If those tools do not handle N's in the assembly, I advise you to use similarity search (using BLAST) against known mitochondrial sequences of closely related species and perform a manual review of those similarity searches. Or, you may also look for other annotation tools that can fit well to your case.

Best, Pedro