Dealing with primer modifications

[sscoster]

Hi,

I'd love to use minibar to help me demultiplex custom barcodes and primers with ONT sequencing. I saw a note on the documentation that IUPAC codes Y and R are recognized, but I also have W. Is that recognized?

And then in addition, my primer code has internal deoxyInosine and I'm trying to figure out how to deal with this.

Do you have suggestions for me to try for these issues?

Many Thanks!

[jbh-cas]

Hello,

The other authors of our paper specified the YR usage for minibar but I see in papers such as "Molecular Tools to Identify and Characterize Malignant Catarrhal Fever Viruses (MCFV) of Ruminants and Captive Artiodactyla" the use of W M and K as well as deoxyInosine which I believe is best matched as N, i.e, any of ACGT.

We can look at adding those to minibar's equality map. Are you familiar with any other primer extensions that find common usage.

best,

jh

[sscoster]

Hi there, It would be so wonderful if you could add these other degenerate nucleotides to the minibar equality map! This would really help out my analysis. I haven't been working with many different universal primers, so I can't speak to which other degenerate nucleotides are commonly used. Best, S

…

On Tue, Dec 6, 2022 at 3:07 PM Jim Henderson ***@***.***> wrote: Hello, The other authors of our paper specified the YR usage for minibar but I see in papers such as "Molecular Tools to Identify and Characterize Malignant Catarrhal Fever Viruses (MCFV) of Ruminants and Captive Artiodactyla" the use of W M and K as well as deoxyInosine which I believe is best matched as N, i.e, any of ACGT. We can look at adding those to minibar's equality map. Are you familiar with any other primer extensions that find common usage. best, jh — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOUXBD5GYA4JSUBUMUNGU43WL6MHTANCNFSM6AAAAAASUZ2ELY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jbh-cas]

Version 0.24 adds N and the other 2 base equivalent letters available in the primer sequence.

From 0.24 README:

Primer sequences can contain, in addition to the nucleotide identifiers ACGT, the IUPAC codes Y, R, W, S, M, K or N. In the case of Y, a C or T counts as a match. And for R, A or G counts as a match; likewise W: AT, S: CG, M: AC, K: GT, and N any of ACGT. Both primers are assumed to be the same length; consequently, there is one edit distance value used for the primers. Barcodes are also assumed to be the same length.