Choosing start position for circular scaffold

[jmhallas]

Hi,

I was wondering if there is a way to choose a specific gene to start the completed mtDNA genome from? For example, start the scaffold at tRNA-Phe. In the scaffold getorganelle assembled for me tRNA-Phe is at position 11,175, and I would like it to be at position 1.

Thank you for your time and suggestions.

-Josh Hallas

[JianjunJin]

Hi, thanks for reaching out. I'm sorry that we don't have a function for reseeding a circular sequence currently, which may involve accurate annotation.

[jmhallas]

Hello, I don't know what you mean by reseeding? I am using a complete mtDNA genome with an annotation as a seed but the seed starts at different gene than my assembled mtDNA from getorganelle. Is there a way to get my new assembly to start at the same gene? This is the command I'm using get_organelle_from_reads.py -1 DS18041_R1.fastq.gz -2 DS18041_R2.fastq.gz -k 21,45,65,85 -s Hassanin_2012_JN632670.fasta --genes gene.fasta -F animal_mt -t 32 -o odocoileous_mitogenomes_4

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On Wed, Jan 18, 2023 at 9:12 AM JianjunJin ***@***.***> wrote: Hi, thanks for reaching out. I'm sorry that we don't have a function for reseeding a circular sequence currently, which may involve accurate annotation. — Reply to this email directly, view it on GitHub <#230 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQOUKLW3C6X4MLTHAP2ZL4TWTAP7ZANCNFSM6AAAAAAT6WWYAA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[JianjunJin]

Sorry about the unclear of what I meant by using an improper word reseed - I meant to restart a circular sequence.
I totally got your point. The clear answer should be there is currently no way of doing that automatically through GetOrganelle.

I have been thinking about that because there are many demands, including getting a new start for a circular genome and picking the structure looking more like the reference when there are multiple structures. But I can only work on that after pushing on other issues. It is more like a downstream treatment but will be useful. I can keep you posted if it is available, but it will be a while.

[jmhallas]

Thank you for clarifying. It would be a nice feature. I was hoping I just might have missed something in the getorganelle manual. Thanks again.

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On Wed, Jan 18, 2023 at 1:59 PM JianjunJin ***@***.***> wrote: Sorry about the unclear of what I meant by using an improper word reseed - I meant to restart a circular sequence. I totally got your point. The clear answer should be there is currently no way of doing that automatically through GetOrganelle. - I have been thinking about that because there are many demands, including getting a new start for a circular genome and picking the structure looking more like the reference when there are multiple structures. But I can only work on that after pushing on other issues. It is more like a downstream treatment but will be useful. I can keep you posted if it is available, but it will be a while. — Reply to this email directly, view it on GitHub <#230 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQOUKLS22CRJQCS34VPH76TWTBRULANCNFSM6AAAAAAT6WWYAA> . You are receiving this because you authored the thread.Message ID: ***@***.***>