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Hi,
Thanks for developing freddie tool!
I was trying to apply freddie to our cancer dataset, however, currently I'm experiencing some issues.
1) Our data are nanopore long reads and previously w…
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Dear Canu Team,
I have recently compiled a more recent version of Canu (-- canu snapshot v2.3-development +162 changes (r10433 c61ebbb7a5f90abb9c034650e2fd95642138de31) to assemble small amplicons…
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Hi,
I have a question about the genotyping of single cells with the `sc_mutations` function. Are UMIs used there to collapse duplicates or correct sequencing errors? If not, is it a planned feature…
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I have some nanopore sequences stored in pod5s.
I first converted pod5 to fast5, then used multi-to-single-fast5 command to have single-read fast5s, then I try to annotate the fast5 using the fast…
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Hello
I am currently trying to compare simplex base calling with duplex base calling using Dorado. I am using raw binary outputs from the Nanopore sequencer (.pod5 files) with R10.4 flow cell.
F…
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**Describe the bug**
I am trying to use phables on my metagenome assembly, assembled with metaFlye.
**To Reproduce**
Steps to reproduce the behaviour, including the
1. Command executed
```
pha…
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Hi,
I get the following error running
```
./modkit pileup \
~/Data/nanopore/mysample.pass.sorted.bam \
~/Data/nanopore/mysample.pileup.bed \
--ref ~/Data/hg38.fa \
--cpg
> calculated chunk…
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Hello,
Thanks for developing this tool! I'm looking to run it with nanopore long reads. Have you tried using it for that before? Could you share any experiences or insights regarding its application…
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Hello, i am trying to use NanoPlot on fastq files created from Nanopore reads to filter the reads, create plots and create a summary file.
But i get the error: --maxlength: command not found
What c…
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Hi,
Thank you for making a pipeline for nanopore reads analysis.
I have some fasta sequence files from the nanopore sequencer that I want to analyse using the pipeline. I had nanopore amplicons …