Ka Ming Nip
Ka Ming Nip
Similar to #161: If you install from bioconda, it is less likely to have installation issues. For example: ``` conda create -n nanosim conda activate nanosim conda install -c bioconda...
Hi Chris, Can you try installing version 0.21.3 of scikit-learn and re-run your simulation? ``` conda install scikit-learn=0.21.3 ``` If the simulation doesn't work, then try upgrading scikit-learn to the...
As far as I can tell from the code, the values for options `--min_len` and `--max_len` are not used at all in the transcriptome mode (unlike genome and metagenome modes)....
Thanks Baraa! I agree with you. I have suspicions that this is an issue when I was reading through `simulator.py` recently. @SaberHQ and I will look into it!
Hi @jlipovac , It looks like this is related to pull-request #167, which is pending review now. Ka Ming
Hi @jlipovac , I have merged the PR. The changes should be in the master branch now. Let us know if you still have any issues. Ka Ming
The pretrained models in NanoSim were made using an older version of `scikit-learn` (e.g.
You are right, it should be an underflow instead of an overflow. The FASTQ has only 3 reads.
Hi @schorlton, Are you seeing different FASTA header formats in the final output (i.e. `rnabloom.transcripts.fa`) of different assemblies? Or, you mean different output FASTA files from the same assembly have...
Ah, ok. The reason why you see this header style in some but not others is because some assemblies may have ended at an earlier stage. To resolve this issue,...