NanoSim
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bcgsc
Nanopore sequence read simulator
I did a fresh install of conda (via miniconda3) and installed nanosim. When running, I get this error: ``` Traceback (most recent call last): File "/home/philae/.local/share/miniconda3/bin/simulator.py", line 2400, in main()...
Hi, I'm trying to simulate metagenome reads (including chimeric reads) using pre-trained model and I succeeded in it but I got fasta file of simulated aligned reads with reads that...
Hi there! I was running some simulations today with nanosim until I stumbled upon some issue that I thought may be worth pointing out here. First of all, I was...
Hi @cheny19, I noticed the discription of NanoSim was a Nanopore sequence read simulator. And I wonder harness a software to generate some Nanopore reads with given a genome or...
Hi there, I am trying to simulate nanopore amplicon reads (~6.5 kbp longest amplicon, ~37 kb total sequence) but the simulation part seems to hang and never proceed. I was...
I'm getting some index out of range errors, possibly because of setting the same value (or too close?) for `-min` and `-max`: `-min 10000 -max 10000`: ``` 2022-04-21 13:17:35: Start...
[NanoSim_installation_problems_15April2022.txt](https://github.com/bcgsc/NanoSim/files/8491882/NanoSim_installation_problems_15April2022.txt)
In line 1505 of the `simulator.py` script: https://github.com/bcgsc/NanoSim/blob/23911b67ce4733f0468ac26296e25348e3b73b4b/src/simulator.py#L1504-L1506 The seed is reset before each process/thread is started. This overrides the setting of the random seed in here: https://github.com/bcgsc/NanoSim/blob/23911b67ce4733f0468ac26296e25348e3b73b4b/src/simulator.py#L2180-L2181 It also...
Hi NanoSim Team, I'm simulating reads in transcriptome mode, and I want to restrict the minimum and maximum length of simulated reads with "--min_len 3400 --max_len 3450" options. But, It...
Here is my command to simulated reads: ./simulator.py transcriptome -rt /data/hgyi/work/RNAseq_quantTool/Homo_sapiens.GRCh38.cdna.all.fa -c ../pre-trained_models/human_NA12878_dRNA_Bham1_guppy/training -e ../pre-trained_models/human_NA12878_dRNA_Bham1_guppy/expression_abundance.tsv -n 100000 --no_model_ir. I found most of reads simulated did not aligned to (not even...
