Simon Hegele

Hey you, I also had issues building a custom database. Apparently there have been stuctural changes to NCBI, that Kraken2 has not been adapted to. If that is the reason...

Hey, you don't need this command since the database you downloaded is already build, you can start classifying right away :)

Guess you are interested in HIV-viruses. Download the prebuild Viral database or the Standard database from https://benlangmead.github.io/aws-indexes/k2

Seems to be a common issue. Apparently NCBI changed the way the required data can be retrieved and Kraken2 hasn't been adapted to it. Try one of the pre-built databases,...

@Nifaste had it right, you can specify the desired python version when using pip. Instead of: pip install AlignQC Try: pip2.7 install AlignQC (need python 2.7 obviously)

Hi, sry, my message missed some crucial information. And I digged in further what is the problem. The error message: "Please make sure transcript IDs in the expression profile match...

@SaberHQ I used NanoSim for the quantification. `read_analysis.py quantify -i ont.fastq -rt rna.fna -o nanosim_out -t 56 -e trans` and then the simulation with `simulator.py transcriptome -rt rna.fna -rg GCF_000001635.27_GRCm39_genomic.fna...

Hi, sorry for my late reply. Read simulation: `simulator.py transcriptome -rt transcriptome.fasta -e chr1_abundance.tsv -c model/training -n 1000000 --no_model_ir -t 128 -o perfect --perfect` Model creation: `read_analysis.py transcriptome -rt transcriptome.fasta...

Thank you for your reply. I think it it is generally a good idea to have the DGB constructed both from long and short reads so the long reads get...