search

AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
142 stars 37 forks source link

Problem about the virus location #52

Open mujiezhang opened 2 years ago

mujiezhang commented 2 years ago

Hi, I am using VIBRANT predicting viruses from bacteria genome. But the result only show the virus is in a certain fragment, but I do not konw the fragment is in which genome contig and the virus begins with which bp and ends with which bp. In a word, I could not locate the predicted virus in the bacteria genome exactly.

KrisKieft commented 2 years ago

Hi,

Which version of VIBRANT are you using? The most recent v1.2.1 will generate a "prophage coordinates" file that has the genomic location (start and stop) of the extracted prophage. Updating should solve this for you. Likewise, the term "fragment" is appended onto the name of the host scaffold, so whatever name comes before "_fragment_#" will be the scaffold that the prophage was extracted from.

mujiezhang commented 2 years ago

Oh, I find it. Really thanks for your helpful reply!

发送自 Windows 10 版邮件应用

发件人: Kris Kieft 发送时间: 2021年7月6日 22:28 收件人: AnantharamanLab/VIBRANT 抄送: mujiezhang; Author 主题: Re: [AnantharamanLab/VIBRANT] Problem about the virus location (#52)

Hi, Which version of VIBRANT are you using? The most recent v1.2.1 will generate a "prophage coordinates" file that has the genomic location (start and stop) of the extracted prophage. Updating should solve this for you. Likewise, the term "fragment" is appended onto the name of the host scaffold, so whatever name comes before "fragment#" will be the scaffold that the prophage was extracted from. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.