User: Ömer An
Ömer An • 200
- Reputation:
- 200
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- Singapore
- Website:
- https://csibioinfo.nus...
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- 1 week, 3 days ago
- Joined:
- 7 years, 9 months ago
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Posts by Ömer An
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... The link does not work either. ...
written 7 weeks ago by
Ömer An • 200
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Comment:
C: correcting for a batch in DESeq2
... if you want to completely ignore the change due to treatment, then remove it:
dds <- DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~ batch) ...
written 3 months ago by
Ömer An • 200
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3
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3
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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 5 months ago by
Ömer An • 200
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1
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... miRge link does not work ...
written 5 months ago by
Ömer An • 200
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2
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1.3k
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2
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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 5 months ago by
Ömer An • 200
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3
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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 5 months ago by
Ömer An • 200
0
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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 5 months ago by
Ömer An • 200
1
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2
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... And what's the difference between refGene and ncbiRefSeq gtf? ...
written 8 months ago by
Ömer An • 200
0
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2
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803
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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 9 months ago by
Ömer An • 200
0
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2
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4.3k
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2
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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 10 months ago by
Ömer An • 200
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For How to identify non-expressed genes in microarray?
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13 months ago,
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For A: how to extract sample id with bcftools or vcftools
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For How to identify non-expressed genes in microarray?
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For How to identify non-expressed genes in microarray?
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For How to identify non-expressed genes in microarray?
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For How to get the coding sequence of each isoform of a gene?
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For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
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