User: Ömer An

gravatar for Ömer An
Ömer An200
Reputation:
200
Status:
Trusted
Location:
Singapore
Website:
https://csibioinfo.nus...
Last seen:
1 week, 3 days ago
Joined:
7 years, 9 months ago
Email:
b*****@gmail.com

Posts by Ömer An

<prev • 62 results • page 1 of 7 • next >
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Comment: C: How to plot coverage and depth statistics of a bam file
... The link does not work either. ...
written 7 weeks ago by Ömer An200
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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 An200
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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 An200
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Comment: C: best STAR options for miRNA mapping?
... miRge link does not work ...
written 5 months ago by Ömer An200
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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 An200
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Answer: A: software of single-cell RNA-seq from fastq or fasta
... 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 An200
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Comment: C: CellRanger Make Counts Expected Cells
... 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 An200
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Comment: C: How to download mm10 GTF file with the gene id and gene name using UCSC table br
... And what's the difference between refGene and ncbiRefSeq gtf? ...
written 8 months ago by Ömer An200
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Comment: A: How to analyze the RNAseq paired samples with DESeq2?
... 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 An200
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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 An200

Latest awards to Ömer An

Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: how to extract sample id with bcftools or vcftools
Popular Question 15 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Voter 15 months ago, voted more than 100 times.
Popular Question 20 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 21 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How to get the coding sequence of each isoform of a gene?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Supporter 4.0 years ago, voted at least 25 times.
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA

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