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This was never migrated to the toolshed.
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Hello,
I was wondering how exactly VirSorter defines a prophage regions and if there is a way to get the coordinates of the prophage regions identified?
Thanks,
Niamh
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Hi,
Thanks for making this tool! I'm a little curious as to how to correctly interpret the prophage/host ratio in the output file. In your opinion, would this value be valid to rely on? Or rather, …
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Hi, Wenchen, prophage hunter is a nice tool for prophage detection and I have used it in web version a few years ago. However, I have several questions about it.
1. Is the web of prophage hunter sti…
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Current sets of prophages are probably highly redundant, should use some kind of CD-HIT like clustering procedure to get a set of unique prophage sequences
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When I downloaded the zip file in the link(https://github.com/NancyZxll/temperate-phage-active-prophage-detection/releases/tag/V1.0) and ran it according to the readme, the following error message app…
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I tried running your Prophage_Tracer for the first time today and I got this error
awk: cmd. line:1: fatal: division by zero attempted
I followed your directions to index with bwa, then map with b…
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Hi,
I am currently applying PropagAtE (default parameters) to gut metagenomic data and I am struggling to understand which filters to apply to the output .tsv files. I see that in the output .tsv f…
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Hi, I got some MAGs using the binning method. I have identified prophage in MAG, and want to analyze the activation prophage. First, the MAG includes some contigs other than the whole genome sequence …
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I'm confused a little bit about the input fils -f: input genomes/scaffolds and -v: prophage coordinates input from VIBRANT. I want to analyze the activation prophage in several case/control samples bu…