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Clairvoyante is a new deep-learning approach to SNP and indel calling designed for long read sequencing (https://www.nature.com/articles/s41467-019-09025-z). We should implement this in our pipeline …
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@iqbal-lab are there standard filters you would like to apply? If not, how do you suggest we go about determining what filters to use?
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Hi,
When I use the nanopolish 0.13.2 to detect the polyA tail, I get saome issues. I can finish nanopolish index. Then, I run 'nanopolish polya'. The errors are as follows:
How can I fix i…
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Hiya,
I saw the preprint on bioRxiv and thought I'd give GALA a go. I've ran into two issues though pretty right off the bat.
I've two different genome assemblies listed in drafts.txt, with fu…
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Using a fresh conda install under ubuntu 16 with 88 cores and 512GB RAM
FR: could you please add a '-v / --version' argument to your tools to get the pipeline version
> longread_umi nanopore_pipel…
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CurrentlY: Nextflow pipeline for analysis of Nanopore reads (from RNA/cDNA/DNA)
should be: Nextflow pipeline for analysis of Nanopore direct RNA reads
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Hi:
Sorry for disturbing you again.
I have noticed that A **blacklist**(contains tandem genes of tair) is required for filtering false positives during chimeric RNA detection in pipeline.
1. Unfor…
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Dear developers,
We are running a DNA methylation analysis using Nanopore data and the pipeline appears to work fine. I just wanted to double-check and get a confirmation regarding read trimming.
…
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Hi PengNi,
I am trying to run deepsignal on our HPC GPU, but I get this error:
```
# ===============================================
## parameters:
input_path:
/home/ls760/nanopore/us/sc…
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The pipeline was working well for one library and then repeated on another library and then an error came during the assign fast5 creation from the sorted alignment file. I can see the BAM file looks …