User: Ömer An
Ömer An • 200
- Reputation:
- 200
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- Location:
- Singapore
- Website:
- https://csibioinfo.nus...
- Last seen:
- 3 days, 20 hours ago
- Joined:
- 7 years, 4 months ago
- Email:
- b*****@gmail.com
Posts by Ömer An
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Comment:
C: STAR or Bowtie for small RNA seq?
... or NovoAlign? should we also consider it in the comparison, if not, why so? ...
written 17 days ago by
Ömer An • 200
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... miRge link does not work ...
written 17 days ago by
Ömer An • 200
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Comment:
C: Cellranger count fails at mapping
... I don't think this could be a problem. I am also running cellranger using symlinks for `--fastqs` parameter and it works fine on [CSI NGS Portal][1]
[1]: https://csibioinfo.nus.edu.sg/csingsportal ...
written 29 days ago by
Ömer An • 200
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... Hi,
You can use scRNA-Seq pipeline for 10x samples on [CSI NGS Portal][1] starting from fastq files all the way to the matrix folder that Seurat can read as the input. Everything is fully automated.
[1]: https://csibioinfo.nus.edu.sg/csingsportal ...
written 29 days ago by
Ömer An • 200
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... Thanks for sharing. Indeed I was also curious to know the impact of this parameter, and have tested for this myself. I have run it with default parameter and with `--expect-cells=10000` and compared the results. I got similar statistics in the Summary page of `web_summary.html`, although the Barcode ...
written 29 days ago by
Ömer An • 200
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... And what's the difference between refGene and ncbiRefSeq gtf? ...
written 3 months ago by
Ömer An • 200
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... You can use [CSI NGS Portal][1] for a full Differential Expression analysis using DESeq2.
[1]: https://csibioinfo.nus.edu.sg/csingsportal ...
written 4 months ago by
Ömer An • 200
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Answer:
A: input for rMATS
... I can suggest you to try rMATS pipeline to analyse your RNA-Seq data using [CSI NGS Portal][1].
You don't have to worry about read length this way as it is auto calculated.
[1]: https://csibioinfo.nus.edu.sg/csingsportal ...
written 5 months ago by
Ömer An • 200
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... I can suggest you to try scRNA-Seq pipeline to analyse your 10x single cell RNA-Seq data using [CSI NGS Portal][1].
You get individual as well as aggregated output files processed by Cell Ranger software.
[1]: https://csibioinfo.nus.edu.sg/csingsportal ...
written 5 months ago by
Ömer An • 200
0
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... Very useful tutorial!
I have just integrated the most popular two of these tools (ngsplot and deepTools) to the [CSI NGS Portal][1].
You can generate all the plots for your RNA-Seq/ChIP-Seq samples in a comprehensive, robust and quick way with a few clicks using the portal.
[1]: https://csibio ...
written 5 months ago by
Ömer An • 200
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