NanoSim

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Can NanoSim be applied to simulate single cell Nanopore reads

1

Hi, Thanks for the great tool. As the title, I'm wondering if this tool can be applied to simulate single cell Nanopore reads. I'm thinking to generate bunch of transcripts...

yuntianf

Hello all, As we discussed via Slack, I found that the phred quality scores when outputting perfect reads appear to vary as expected for when simulating error reads, instead of...

lcoombe

Hi, In **NanoSim**, inappropriate dependency versioning constraints can cause risks. Below are the dependencies and version constraints that the project is using ``` _anaconda_depends=2019.03=py37_0 _ipyw_jlab_nb_ext_conf=0.1.0=py37_0 _libgcc_mutex=0.1=main genometools-genometools htseq=0.11.3=py37hb3f55d8_0 joblib=1.1.0=pyhd3eb1b0_0 last=874=h8b12597_3...

PyDR-Tool

Hello! I tried to use docker container for nanosim to generate transcripts. Here is the command I used (mouse genome): ```read_analysis.py transcriptome -i "/groups/dog/anastasia/data/data_ciri-long/CRR194209.fq.gz" -rg "/groups/dog/anastasia/nanosim/GRCm39.genome.fa.gz" -rt "/groups/dog/anastasia/nanosim/gencode.vM34.transcripts.fa.gz" -annot "/groups/dog/anastasia/nanosim/gencode.vM34.annotation.gtf.gz"...

aerusakovich

Questions about the usage and processing of the expression profile

1

Hello, I am simulating reads in transcriptome mode. For this purpose, I have created an expression profile in the specified format. The read counts generated per transcript are different from...

joyceFunk123

Reading the simulated_aligned_reads

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I want to analyze the output of NanoSim based on simulated_aligned_reads and compare it with the input of the human reference genome from GRCh37 and using the pre-trained human guppy...

Evandio-Martin

Variation in relative abundances of simulated Zymo mock microbes

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Hi, We've been trying to simulate Zymo mock communities using your "even" pre-trained model. We've consistently found *Staphylococcus aureus* to be seemingly undersimulated, while *Cryptococcus neoformans* appears to be oversimulated....

ezherman

Stuck at the simulation step

5

Hi there, Thank you for developing this handy tool; I've been using it for a long time. Recently, I wanted to perform a more challenging test on my tool by...

HLHsieh

Hi, Would be possible to add an option to gzip intermediate fastq files as they are generate by `simulator.py`? best nic

nicolo-tellini

How many threads and memories required at training stage?

1

Thank you for your development. I am using Nanosim to simulate ONT data, I use 32 threads and 256GB memory to run training stage, but it reported out of memory...

yaoxkkkkk