Comments (1)
bcftools and samtools have separate conda installations. Also, needed to install the anaconda channels conda-forge and bioconda into the local environment, do download the correct libraries for the version of bcftools). (https://www.biostars.org/p/9480029/)
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Related Issues (20)
- Clean Mummer4 run from the sample data HOT 1
- R-Shiny/Shinyserver web app for pH experiment circos plots HOT 3
- Add a GUI menu for selecting a BioProject and user input using the tkinter python package. HOT 2
- Annotation step for .VCF data HOT 8
- IGV display of individual mutant regions
- Mutation rate analysis HOT 4
- Generate a collection of dotplots HOT 1
- Multi-threading for the workflow steps HOT 1
- NCBI Datasets download configuration HOT 1
- Make the MUMMER4 runs into a .sh executable HOT 9
- trimmomatic error from the script HOT 1
- Automated workflow should run in the system, rather than user home directory. HOT 1
- NexteraPE-PE.fa file should be accessible to the trimmomatic wherever it runs.
- Mummer runs generically based on a single RefSeq genome and genus uid. Integrated into the overall workflow.
- Download RefSeq genomes by strain (rather than by ncbi-datasets designated genome)
- Get SRA metadata along with the reference and SRA run downloads HOT 5
- Annotation specified by user needs to be implemented HOT 5
- Re-adjust user's project folder file path based on user's preference HOT 2
- Set up connection to the GitHub repo HOT 2
- use gitclone to install and troubleshoot the repo
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