Bio-Tradis
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sanger-pathogens
A set of tools to analyse the output from TraDIS analyses
Hi, I have two libraries that I am having problems with the bacteria_tradis mapping for. I have used cutadapt to trim the transposon (and adapters) from the reads and selected...
I recently installed biotradis using conda Name Version Build Channel biotradis 1.4.5 hdfd78af_5 bioconda I noticed that I had an issue with reads with clipping (which I think you've seen...
Hello I found a small bug, if I provide the input file ending in the extension ".tsv" to bacteria_tradis it runs without complain but it reports zero reads mapped. However,...
When using the Docker image within Singularity, invoking tradis_merge_plots produces the error: ```shell sh: 1: tradisfind: not found ``` This is not surprising as I cannot find an instance of...
Not sure if anyone else is seeing this or if this is fixable from the BioTraDIS side, but whenever I try to run the tradis_comparison.R script it has issues with...
Hi, We've been running BioTraDIS on a .embl file which contains a chromosome and two plasmids ([GCA_000008865.2.txt](https://github.com/sanger-pathogens/Bio-Tradis/files/10115303/GCA_000008865.2.txt)). On our data the command bacteria_tradis works fine and as would be expected...
I have tried install biotradis through conda using the following command: conda install -c bioconda biotradis however it wasn't able to resolve the environment and this error message came up:...
Hi, I have issues with the essentiality function not returning any essential genes due to not finding an intersection point. I attach the histogram of the sample and you can...
on a new machine, fresh conda install: Any thoughts on how to rectify? Thanks phil@BA085063:~$ tradis_comparison.R -h Loading required package: edgeR Loading required package: limma Error: package or namespace load...
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A set of tools to analyse the output from TraDIS analyses