Mutation linkage

[zhangqi123-gif]

Hello, I want to use novoplsty to assemble numts, but the result I got did not store numts file, the following is my configuration file and the result I got, the version I used is NOVOPlasty4.3.5.pl, what is the cause?

[ndierckx]

The file jj4_mitogenome.fasta, was it produced from the same dataset with NOVOPlasty?
And are you expecting to find NUMTs, because it is not abnormal to not find NUMTs...
Because it designed to find heteroplasmy not NUMTs, so only recent NUMTs will interfere with the heteroplasmy detection and thereby detected with this method, ancient NUMTs will probaply be removed before the NUMT assembly module is activated

[zhangqi123-gif]

First of all, thank you for your reply, I will describe my situation specifically according to your reply.
Yes, jj4_mitogenome.fasta was produced from the same dataset with NOVOPlasty，and I really want to find all NUMTs, especially ancient NUMTs. After reading your reply, I understand why I can't find NUMTs, which makes me a little sad.
In addition,i have two questions to confirm. First, if my jj4_mitogenome.fasta has used the same dataset but the assembly software has not used NOVOPlasty, can I also use the mitochondrial genome generated by this procedure? The second problem is that my output file should be output as a blank numtfile or no numtfile at all.

[ndierckx]

I checked the files you send, indeed no NUMTs were detected. There were quite a lot of possible heteroplasmy positions, although I think some could be sequencing errors. But again it is not designed to find NUMTs, so very recent NUMTs that have no sequence difference with the original mitochondrial sequence will never be detected.

I also noticed that your sequencing depth is not that high, how much coverage are you expecting to have of the nuclear genome?

[zhangqi123-gif]

My sequencing depth for the nuclear genome is 30x

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---- Replied Message ---- | From | Nicolas ***@***.***> | | Date | 11/13/2024 16:16 | | To | ***@***.***> | | Cc | ***@***.***>***@***.***> | | Subject | Re: [ndierckx/NOVOPlasty] Mutation linkage (Issue #234) | I checked the files you send, indeed no NUMTs were detected. There were quite a lot of possible heteroplasmy positions, although I think some could be sequencing errors. But again it is not designed to find NUMTs, so very recent NUMTs that have no sequence difference with the original mitochondrial sequence will never be detected. I also noticed that your sequencing depth is not that high, how much coverage are you expecting to have of the nuclear genome? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[ndierckx]

If that is the case there is definitely not many NUMTs, because it would have found it quite easily, 0.006 is way to loo low, NUMTs would have a much higher fraction. But if there are no ancient NUMTs, why would you expect more recent NUMTs? You can always align all the reads to mitochondrial assembly and visually inspect in IGV if there are possible NUMTs aligned..

[zhangqi123-gif]

Thank you very much for your reply. I think what you said makes sense. I will try using IGV or other software to assemble numt. Additionally, there is one more question that I am very curious about. In the log of this software, there are listed both aligned reads and assembled reads. If I could identify these two types of reads based on the log file and remove the assembled reads from the aligned reads, would it be better to use the newly obtained reads to assemble numt. Or I think that in the actual assembly process, some reads from numt will also participate in the assembly process (such as sequences that are very similar or even completely identical to mitochondrial homologous sequences to construct consensus sequences)

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---- Replied Message ---- | From | Nicolas ***@***.***> | | Date | 11/13/2024 16:40 | | To | ***@***.***> | | Cc | ***@***.***>***@***.***> | | Subject | Re: [ndierckx/NOVOPlasty] Mutation linkage (Issue #234) | If that is the case there is definitely not many NUMTs, because it would have found it quite easily, 0.006 is way to loo low, NUMTs would have a much higher fraction. But if there are no ancient NUMTs, why would you expect more recent NUMTs? You can always align all the reads to mitochondrial assembly and visually inspect in IGV if there are possible NUMTs aligned.. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[ndierckx]

Hi,

Aligned reads could indeed contain some NUMTs sequences, bit there not being stored so you can't retrieve them...
But I don't think filtering those out will help assembling NUMTs. Maybe there even are no NUMTs...