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I'm wondering if there is concise documentation somewhere for reproducing the exact analysis of the TCGA/GTEX data in this [paper](https://www.nature.com/articles/nbt.3772) (but with new samples).
h…
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# [BI] RNA-seq data processing using nf-core pipeline | Keun Hong
Link: nf-core rnaseq pipeline
[https://keun-hong.github.io/bioinformatics/rna-seq-nf-core/](https://keun-hong.github.io/bioinformati…
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### Description of feature
Hi, I was wondering if you guys have thought to give the pipeline an option to use variants called from a DNA-seq(typically wgs) pipeline to use as input into "ASE read cou…
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Hi, thank you so much for the great tool.
I'm trying to apply longshot on long-read RNA-seq data (Iso-seq data from PacBio HiFi reads).
I ran the pipeline with default options and got ~30% reads …
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Hi Thanks for the great work!
I tried to call somatic variant using clairS, but the output vcf only returned 1 variant on Y chromosome..
My datasets are PacBio long-read scRNA-seq with a bit low co…
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### Description of feature
Hi from Lund!
We discussed Tomte today, and what would be needed for us to get it into production.
One thing that came up is that we would want a contamination check.…
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I try to run the RNA-seq pipeline, but got this message:
```
Seq2science has trouble querying the assembly providers. Try again in a bit.
To see the error stack trace run seq2science with --debug…
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Hi,
I'm using drop 1.3.3 in order to do aberrant expression analysis. However during outrider execution with 2 bam data and 9 external counts, I'm getting the following error:
```
[Tue May 30 16:…
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See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)
- assembly accession number: GCF_040414725.1
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Determine the requirements and potential options for the basis of the Pangenome Annotation RNA-seq pipeline.