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I am working on converting an old pipeline that used guppy_basecaller, tombo, and meme to process a methylation experiment.
I have the data in fast5 format. In the past, I used guppy as follows.
`…
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The suggestion of changing output of assay from 'information content entity' to 'data item' is the result of assay harmony task.
In total 181 OBI assay terms, 133 have logical definitions to fit t…
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i'm a newbie to sequencing analysis & working on a pooled sample project for the first time. i've found [this slide deck](https://yeamanlab.weebly.com/uploads/5/7/9/5/57959825/snp_calling_pipeline.pd…
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editor preferred term: Illumina MiSeq FGx
alternative terms: MiSeq FGx
textual definition: First fully validated sequencing system for forensic genomics (FGx).
definition source for the textual def…
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editor preferred term: Illumina NextSeq 500
alternative terms: NextSeq 500
textual definition: Desktop sequencing system to analyze whole genomes, exomes, and transcriptome.
definition source for t…
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ideally there would be a script to generate test datasets from genome sequence data.
classic approach is to take reads from isolate genomes and mix them in known abundances.
need to get isolate genome…
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It looks like a lot of fusions are missed. For example very well known fusions that are always missed by breakfast:
- DUX4-IGH is not found by breakfast in NALM6 cell line (RNA-seq from CCLE).
- …
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**New term details**
For us to assess a new term request we require the following details:
```
Term name - relative amount of nucleic acids in the gradient position
Structured comment name - gradi…
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Dear dada2 enthusiasts,
I'm pretty new to dada2 so I would like to hear some opinions from those who are experts and use dada2 regularly about my issue analysis.
I have tried using filterAndTrim…
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Hi Dr.Zhang,
I am working on paired-tag data and as recommended, trying to analyze paired-tag DNA sequencing data using snapATAC. I wonder how I can load the results of paired-tag data("barcodes.ts…