User: CY

gravatar for CY
CY370
Reputation:
370
Status:
Trusted
Location:
United States
Website:
https://www.dna-ghost....
Last seen:
18 hours ago
Joined:
3 years, 11 months ago
Email:
c********@hotmail.com

Posts by CY

<prev • 216 results • page 1 of 22 • next >
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Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
... DESeq2 uses GLM with negative binomial distibution to model the regressor for variance shrinkage. It is obvious that the expression variance is different for gene with different expression level and a ordinary linear model is not suited. I am wonder if it is possible to model this regressor using LO ...
deseq rna-seq written 9 days ago by CY370
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Comment: C: Archieve of homologous nucleotide sequence across genome
... Sorry for confusion. What I meant is to get the homologous genes / regions across human genome. ...
written 21 days ago by CY370
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Archieve of homologous nucleotide sequence across genome
... I am looking for any reference file that archieves homologous nucleotide sequence (homologous gene) across genome. It could a file harbored in FTP site, a database or a tool for that. Does anyone have any recommendation? P.S. For clarification, what I would like to get is a list of genes or regio ...
sequence written 21 days ago by CY370 • updated 16 days ago by juanjo75es50
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XHMM calls CNV on a number of normal samples
... I recently came across XHMM and got two questions after reading the [paper][1] . How is read depth bias caused by sequence context (probe capture efficiency) normalized? I feel PCA step is not able to do it. Is z-test performed to handle this? The second question is regarding HMM. I noticed that ...
xhh cnv written 28 days ago by CY370
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Comment: C: Library size normalization during CNV calling from genomically doubled tumor tis
... Exactly, by library size I mean the total sequencing depth or fastq size. ...
written 5 weeks ago by CY370
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Comment: C: Library size normalization during CNV calling from genomically doubled tumor tis
... Exactly. If both tumor and normal tissue require same DNA amount during library prep and output roughly same size of fastq, DNA molecule in genomically doubled tumor tissue is "diluted" by requiring the same DNA amount. The genomically doubled region of tumor tissue will have the same depth as in no ...
written 5 weeks ago by CY370
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Library size normalization during CNV calling from genomically doubled tumor tissue
... I realized library size may be an issue and most CNV tools seem to ignore this. Say, we try to call CNV out of a tumor tissue those genome is almost doubled. If we directly compare the depth of each bin between tumor and normal control and the **library size of tumor (fastq size) and normal tissue ...
cnv written 5 weeks ago by CY370 • updated 5 weeks ago by markus.riester480
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Comment: C: Noisy CNV background in old FFPE sample
... Yep. I remembered. Guess you are right. That is one of the reason for getting noisy background. ...
written 7 weeks ago by CY370
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Comment: C: Noisy CNV background in old FFPE sample
... For all I know, long time stored FFPE causes denaturation and fragmentation and shears DNA molecule but not neutralize them (make certain fragment disappear), right? So most of the DNA molecule remain diplod. I did some research and now the impression is that difficulty of de-crossing on FFPE sample ...
written 7 weeks ago by CY370
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Noisy CNV background in old FFPE sample
... This may not be a pure bioinformatics question although I got this problem while trying detecting CNV on a old (over 3 years) FFPE samples. What I observed is very noisy CNV backgroud almost acorss all these old FFPE samples. I did some research and articles shows that this is typical to old FFPE ...
ffpe cnv written 7 weeks ago by CY370 • updated 7 weeks ago by Eric T.2.5k

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Popular Question 6 days ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Detecting variants at very low fractions from ctDNA
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Detecting variants at very low fractions from ctDNA
Great Question 3 months ago, created a question with more than 5,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Student 3 months ago, asked a question with at least 3 up-votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 3 months ago, created a question with more than 1,000 views. For Detecting variants at very low fractions from ctDNA
Popular Question 9 months ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 9 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Prophet 9 months ago, created a post with more than 20 followers. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 11 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 11 months ago, created a question with more than 1,000 views. For STAR genomeLoad issue
Popular Question 12 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Appreciated 14 months ago, created a post with more than 5 votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Good Question 14 months ago, asked a question that was upvoted at least 5 times. For why PCA for RNA-Seq but tSNE for scRNA-seq?
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