Some questions

[Humonex]

Hello,

Thank you for making this program.

I would like to ask whether methphaser can only be used in phasing or can it be used directly in assembly? Because I found that in the meth_phaser_post_processing file, you defined a ‘chroms’, which seems to be only applicable to chr1-chr22. If the number of chromosomes exceeds 22 and there are thousands of chromosomes, can methphaser run normally?

[Fu-Yilei]

Sorry the short answer is no. However, I think it is possible to pipe newly phased reads into assemblers. Cheers, Yilei Fu Postdoctoral Associate Baylor College of Medicine Human Genome Sequencing Center ***@***.*** ***@***.*** Sent from iPhone On Jun 26, 2025, at 7:16 PM, Humonex ***@***.***> wrote:  [https://avatars.githubusercontent.com/u/94833927?s=20&v=4]Humonex created an issue (treangenlab/methphaser#32)<#32> Hello, Thank you for making this program. I would like to ask whether methphaser can only be used in phasing or can it be used directly in assembly? Because I found that in the meth_phaser_post_processing file, you defined a ‘chroms’, which seems to be only applicable to chr1-chr22. If the number of chromosomes exceeds 22 and there are thousands of chromosomes, can methphaser run normally? — Reply to this email directly, view it on GitHub<#32>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADDV4HSCIZMAO5VQ3EK2L6D3FSSRHAVCNFSM6AAAAACAHYJXXKVHI2DSMVQWIX3LMV43ASLTON2WKOZTGE4DCMBYHE3DMMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Humonex]

Thank you. I have another question. I noticed that methphaser can run perfectly on human chromosomes. Can it run on other species with more than 22 chromosomes?