Moderator: igor

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igor6.5k
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Posts by igor

<prev • 932 results • page 1 of 94 • next >
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Comment: C: Making scRNA counts file from barcodes, genes and matrix.mtx file
... Additionally, if you know how you will be analyzing the data, you may want to check the instructions for that pipeline. Many single-cell analysis packages now include a function to read 10x matrix and convert it to the most appropriate format for that package. ...
written 7 hours ago by igor6.5k
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Comment: C: Stranded RNA-seq data visualization in UCSC
... And how are you generating these bedGraphs? ...
written 2 days ago by igor6.5k
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Comment: C: Stranded RNA-seq data visualization in UCSC
... You should check a known housekeeping gene like ACTB or GAPDH before you check some obscure transcript that may not be real. ...
written 3 days ago by igor6.5k
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Comment: C: why do bed files not contain information about the reference?
... Additionally, if you say "hg19" or "hg38", that is actually not entirely accurate either. This post illustrates that problem very clearly: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use Unless you are embedding the entire reference FASTA, you really can't be entirely sure what ...
written 7 days ago by igor6.5k
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Comment: C: Can I convert normalized counts from DESEQ2 into fpkm?
... Non-robust should be the classic FPKMs. If you check the column sums (`colSums`), they should all add to 1M then. ...
written 8 days ago by igor6.5k
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Comment: C: Can I convert normalized counts from DESEQ2 into fpkm?
... Yes. But if the samples are processed separately, you will likely have batch differences. That's a much more complex issue. ...
written 8 days ago by igor6.5k
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Comment: C: Can I convert normalized counts from DESEQ2 into fpkm?
... By default, DESeq2's `fpkm()` will return "robust" FPKMs, which use size factors to normalize instead of taking the column sums of the raw counts. ...
written 9 days ago by igor6.5k
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Comment: C: Transformed cancer cell-lines RNA-seq database
... Thank you. That was very helpful. ...
written 13 days ago by igor6.5k
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Comment: C: Seurat -FindVariableGenes problem
... Yes. Follow the instructions in the tutorial. There are a lot of steps and they have a specific order. ...
written 15 days ago by igor6.5k
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Comment: C: Seurat -FindVariableGenes problem
... This may or may not be causing the error, but `x.low.cutoff` (bottom cutoff on x-axis for identifying variable genes) should probably be higher than 0. ...
written 16 days ago by igor6.5k

Latest awards to igor

Popular Question 10 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 21 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 7 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 8 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 9 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Scholar 10 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Appreciated 3 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)

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