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Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …
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Let's try to use regtools for this.
- regtools junctions-extract function: https://regtools.readthedocs.io/en/latest/commands/junctions-extract/
- parameters to specify:
- `-m 20` (should matc…
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Hi! Thanks for the cool tool!
When I start from estimated read counts from a different pipeline (STAR > featureCounts) should I provide Taiji with raw reads or should I normalise them somehow before …
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At the moment,
```biomedsheets/io_tsv/base.py``` allows
```'WES', 'WGS', 'Panel_seq', 'mRNA_seq', 'total_RNA_seq'```.
However, ```biomedsheets/data/std_fields.json``` defines the following:
…
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Hi there - I'm having some problems running `HaplotypeCallerSpark` on RNA-Seq data.
The tl;dr is that, on some occasions when `HaplotypeCallerSpark` runs out of memory, it finishes successfully, b…
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Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
sam…
-
I am implementing this microtest repository and am wondering what should be placed in the [data path] section in these code blocks:
required_input_files: [data_path]
ngs_input_files: [data…
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Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …
-
Convert the workflow [allele-specific-expression](https://github.com/icgc-argo-workflows/allele-specific-expression) to follow `nf-core` structure and guideline.
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**Are you using the latest release?**
yes
**Describe the bug**
codingquarry should use "-d" for the unstrand stringtie assembly.
But I didn't find the option for the strand-specific informati…