Simon Hegele

Kraken2 seems to classify reads from read pairs separately

1

Tried to classify samples from paired-end sequencing using the command: kraken2 --db {database} --paired {query} {mate} --report {report} --threads {threads} > {out} 2> {log} My samples had 60-80 million read...

DBG construction from short and long reads

2

Hello, and thank you for this amazing tool. I am currently examining different methods of hybrid de novo transcriptome assembly. I constructed various assemblies from mouse data and compared their...

Hi, just wanted to point out, that isONcluster needs to be installed separately, which is not in the installation description. `conda install -c conda-forge -c bioconda isonclust` Best, Simon

Non-zero error rates for perfect reads

2

Hallo dear NanoSim-Team, I simulated 1,000,00 perfect reads and used them to train an error-model. One would expect to find a zero error-rate, however, the model reports an error-rate of...

Feature Request: Checking Input-files

1

Hi, I have been using NanoSim quite a lot lately. I did use it for simulation of nanopore reads or to control the quality of long reads with the read_analysis.py-script...

Transcript ID in reference and expression profile do not match

8

After quantification I tried simulating IDs in expression profile: NM_001001130.3 IDs in reference: \>NM_001001130.3 Mus musculus zinc finger protein 85 (Zfp85), mRNA

Hello, first of all: Thanks for this great tool, that really provides a comprehensive sets of metrics and with neat visualisations as well! For the evaluation of the error rate...