minimap2
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Allow any nucleotide to map to a specific location
Is it possible to allow any nucleotide to map to a specific location without penalty?
For example, we have a reference sequence: G*AC, where * can be any nucleotide. We want to allow GAAC, GTAC, GCAC and GGAC to be mapped to this reference without any penalty.
Is there a way to realise it? Thank you.
The reason we want to do it is that, we have a chemical method that can induce a random mutation to all U, but it is not clear how it will change. Since all the Us are mutated to other bases (too many mutations), the sequences cannot be mapped to reference sequences. The only possible way seems to allow the above scenario to be considered perfect match.
Please let me know what you think. Thank you very much indeed.
Thanks a lot for your timely response.
The reference sequence is an IVT transcript of 1k long. Not very long, but probably long enough to make things complicated.
The mutations are random, for example, ATGT can be mutated to AAGC (first T mutated to A, second T mutated to C)
The mutation should depend on the local sequence contexts, and should be very noisy due to very low nanopore signal quality. It is not clear at this stage how, so we may have to consider the mutation is random at the alignment stage for the time being.
It seems like you would just want to change all the T's to N's in your reference, and then map against that...
But there must be some reason why this simple idea won't work?
It seems like you would just want to change all the T's to N's in your reference, and then map against that...
But there must be some reason why this simple idea won't work?
Not really, I guess. I believe that, N-A, N-C, N-T, N-G are considered as "mismatch" by all other aligners. What I want is that they can be considered as "match" in the problem I study.
Hi, @meng-lab Have you solved this matter yet? I have a pseudou IVT fastq. Similarly, it has very few reads aligned to the reference sequence.
We couldn’t find a solution so far. Sorry for that.
From: kir1to455 @.> Sent: 2024年5月24日 11:41 To: lh3/minimap2 @.> Cc: Jia Meng @.>; Mention @.> Subject: Re: [lh3/minimap2] Allow any nucleotide to map to a specific location (Issue #973)
Hi, @meng-labhttps://github.com/meng-lab Have you solved this matter yet? I have a pseudou IVT fastq. Similarly, it has very few reads aligned to the reference sequence.
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