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katholt
Hi! I tried to prepare a pseudogenome from the VCF file using the script (https://github.com/katholt/RedDog [new_test_marta_pseudogenome.zip](https://github.com/katholt/RedDog/files/8488826/new_test_marta_pseudogenome.zip) /blob/master/snpTable2GenomeAlignment.py). But, the code does not seem to work. When I tried to run...
Hi I'm having some trouble to run redo. Pipeline is falling at inicial stage and I'm getting the following error message: Error: command failed: python convertGenbankToFasta.py Could someone help with...
Hi, I'm having issues with running the pipeline. The first warning message is BiopythonParserWarning. Then next is "No wat to run job"... Upon checking the bam and vcf folders, there...
Hi, We are having trouble getting Red dog to run on our cluster. The pipeline does not start running and we keep getting the error below. Thanks, Kesia Traceback (most...
I am working with a large dataset and have been merging to an existing dataset over and over which up to this point has been working fine. As of my...
Hi, I have the sequence reads of some strains (illumina reads). I want to map these sequences to certain genes (not the whole genome of the reference) and to determine...
Hi, could be any tips to run the RedDog pipeline fast? takes longtime even on only 2 samples. Do I understand it correctly that the processing of each sample include...
Hi everyone. I'm trying to install RedDog pipeline onto my personal computer with linux-based system (and I'm not an expert on Linux). Following the guide at step #2 to obtain...
The tutorial references files that can be obtained from dropbox named RedDog_Extras. However, the link in the PDF can not be clicked and the URL is not provided elsewhere. Furthermore,...
Hi there, I wish obtain recombination based on the pipeline’ file. I thought perhaps I need obtain a strict majority consensus from a bam file, or any other ways. Can...
