search

RockefellerUniversity / RU_GenomicVariants

Working with Genomic Variants
1 stars 2 forks source link

Can I convert Fasta to MAF file? #3

Open mnogueirab opened 3 years ago

mnogueirab commented 3 years ago

I was wondering if I can generate a MAF (mutation annotation file) from a Fasta file which contains the consensus sequences of multiple samples. I ask, because I wanted a best way to define when mutations appear and the frequency that they appear (ideally a comprehensible table to generate graphs in R) . I don't have the fastaq file. The fasta file is all that our collaborator provided us with.

Thank you, Mariana

adamjdluo commented 3 years ago

Hi Mariana I am wondering the fasta file you have is a single consensus sequence derived from multiple alignment results. Is it true? If it is true and I remember right, you would only get the consensus sequence with several degenerated nucleotides for SNPs. So, we may not estimate the allelic frequency directly. From the present information, I think MAF would not fulfill your need. We could try to find out some strategies for you. If you don't mind, we may plan for a brief chat about this question.

JD

mnogueirab commented 3 years ago

Hi JD, The fasta file has many consensus sequences and my aim is to map the mutations between the consensus sequences from each of my samples.

Context: I have three different experimental groups and I sequenced the viral pool ((NGS) that came from each of them (I have many replicates) so in total I have about 15 consensus sequences. The collaborator aligned the consensus sequence to our original virus inoculum and I'm now trying to have an effective way to detect these mutations (instead of doing this manually), afterwards map aa changes in such regions, and see if any of my experimental groups share these mutations or not, how these mutations increase in frequency or not.. etc

Not sure if this information helps, but I was thinking that doing MAF to map the mutations would be the easiest, but if you can think of anything that can be best, I'm happy to try.

Thank you much! Mariana

Mariana Nogueira Batista, PhD

Laboratory of Virology and Infectious Disease

The Rockefeller University

1230 York Avenue

From: Ji-Dung Luo @.> Sent: Wednesday, May 19, 2021 2:10 AM To: RockefellerUniversity/RU_GenomicVariants @.> Cc: mnogueirab @.>; Author @.> Subject: Re: [RockefellerUniversity/RU_GenomicVariants] Can I convert Fasta to MAF file? (#3)

Hi Mariana I am wondering the fasta file you have is a single consensus sequence derived from multiple alignment results. Is it true? If it is true and I remember right, you would only get the consensus sequence with several degenerated nucleotides for SNPs. So, we may not estimate the allelic frequency directly. From the present information, I think MAF would not fulfill your need. We could try to find out some strategies for you. If you don't mind, we may plan for a brief chat about this question.

JD

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_RockefellerUniversity_RU-5FGenomicVariants_issues_3-23issuecomment-2D843775879&d=DwMCaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=rNe0AW_C8vkFmR_gC942_D_vO09neUWVznmJlCQCFEs&m=kxZbwdjJc46t-e2vIe1_y7J-bKbcH62CrYx8FwzeW_M&s=jjGTThGbsW_ZDKRksWQ9srgxQxdaPzCkz1BmKOUjwbc&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ATCAOJFNOPYHTPFPCS2BYFTTONI6TANCNFSM45C7DVJQ&d=DwMCaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=rNe0AW_C8vkFmR_gC942_D_vO09neUWVznmJlCQCFEs&m=kxZbwdjJc46t-e2vIe1_y7J-bKbcH62CrYx8FwzeW_M&s=s0vF4Mg3OYdXbqy-BYONxKtzMbZn62xXHXRY9yjaJn8&e=.