User: Ömer An

gravatar for Ömer An
Ömer An220
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Singapore
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https://csibioinfo.nus...
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Posts by Ömer An

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Batch correction in DESeq2
... In step 2 before normalising with DESeq2, would it help also to filter out the low-read-count genes? Something like: dds = dds[rowSums(counts(dds)) > (2 * n_samples), ] ...
written 5 weeks ago by Ömer An220
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Comment: C: How to plot coverage and depth statistics of a bam file
... The link does not work either. ...
written 4 months ago by Ömer An220
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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 6 months ago by Ömer An220
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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 8 months ago by Ömer An220
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Comment: C: best STAR options for miRNA mapping?
... miRge link does not work ...
written 8 months ago by Ömer An220
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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 8 months ago by Ömer An220
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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 8 months ago by Ömer An220
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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 8 months ago by Ömer An220
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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 11 months ago by Ömer An220
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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 12 months ago by Ömer An220

Latest awards to Ömer An

Popular Question 4 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: how to extract sample id with bcftools or vcftools
Popular Question 17 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Voter 18 months ago, voted more than 100 times.
Popular Question 23 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 3.5 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 3.6 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Supporter 4.2 years ago, voted at least 25 times.
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA

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