input data

[CaroleBelliardo]

Hi iprada,

If the tool is dedicated for DNA-seq data from circular amplification or it can be used to identify circular DNAs from WGS data? Can we use HiFi reads as well?
Is it possible to use minimap for the mapping step ?
thank you

[iprada]

Hi Carole, Thanks for your question. The tool is designed with short reads in mind and should not work optimally for HiFi. If you want to use it with long reads giving a look at our Molecular Cell paper (Henriksen et al.,) might help you. Rasmus Henriksen developed a method to detect circles from long reads and takes minimap2 as input. I also recall skimming through some papers with long reads in mind lately, but I do not work with circles anymore and I am far from being updated with the literature. Some simple literature search might point you to new tools. I hope this helps and happy circle hunting Best, Iñigo From: Carole Belliardo ***@***.***> Reply to: iprada/Circle-Map ***@***.***> Date: Wednesday, 2 August 2023 at 18.06 To: iprada/Circle-Map ***@***.***> Cc: Subscribed ***@***.***> Subject: [iprada/Circle-Map] input data (Issue #95) Hi iprada, If the tool is dedicated for DNA-seq data from circular amplification or it can be used to identify circular DNAs from WGS data? Can we use HiFi reads as well? Is it possible to use minimap for the mapping step ? thank you — Reply to this email directly, view it on GitHub<#95>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AGB2FW2PAHM6YL47AKADWYLXTJ3IJANCNFSM6AAAAAA3BQAESQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>