Hi, I installed nanosim using
conda install -c bioconda nanosim and then tried to run the read characterization using
read_analysis.py transcriptome -i training_reads.fastq -r reference_genome.fa -rt reference_transcriptome.fa -annot reference_annotation.gtf -o training.
However, I get the following error:
Please specify the training reads and its reference genome! ./read_analysis.py : -h : print usage message -i : training ONT real reads, must be fasta files -r : reference genome of the training reads -a : Aligner to be used: minimap2 or LAST, default = 'minimap2 -m : User can provide their own alignment file, with maf or sam extension, can be omitted -b : number of bins (for development), default = 20 -t : number of threads for LAST alignment, default = 1 -o : The prefix of output file, default = 'training' --no_model_fit : Skip the model fitting step
I am sure that the path to the respective files (training_reads and reference_genome) is correct. I tried to provide the input files as absolute as well as relative path but the error remains same. Please help. Thanks
Hi, Thanks for looking into that and pointing out the requirement of fasta file. I did try fasta files as well but got the same error.