User: DVA

gravatar for DVA
DVA480
Reputation:
480
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Location:
United States
Last seen:
2 days, 5 hours ago
Joined:
4 years ago
Email:
s***********@gmail.com

Posts by DVA

<prev • 145 results • page 1 of 15 • next >
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Comment: C: Count 0, 5, 20 covered sites in bam
... Thanks for the help! Appreciate it. ...
written 2 days ago by DVA480
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Comment: C: Count 0, 5, 20 covered sites in bam
... Thank you very much! ...
written 2 days ago by DVA480
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Comment: C: Count 0, 5, 20 covered sites in bam
... Thank you for the comment @genomax, I am looking at individual base level. ...
written 4 days ago by DVA480
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Count 0, 5, 20 covered sites in bam
... Hello, I wonder how to use a bam file to learn how many sites are not covered at all, how many are covered >=5 times and 20 times. We got such stats from our sequencing company, but want to see we can do it ourselves as well. Thank you very much. ...
wgs bam written 4 days ago by DVA480 • updated 4 days ago by Pierre Lindenbaum112k
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Extract the overlap of well-covered regions across multiple samples
... I am looking at somatic mutations across multiple samples, but the samples are not covered equally in many regions. Since we care about comparing the mutation counts between these samples, I would need to consider the uneven coverage -- e.g. sample A has 5X coverage at position 1, while sample B has ...
wgs coverage written 10 weeks ago by DVA480
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Comment: C: Pathway enrichment with differential expression p-values
... Thanks so much for the information! ...
written 3 months ago by DVA480
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Pathway enrichment with differential expression p-values
... Hello All, I have a large set of genes with differential expression p-values (from DEseq2) and directional (up or down-regulated) information. I was wondering if anyone knew of a pathway enrichment analysis program that could make use of all of this information rather than just the gene list? Sorry ...
gene enrichment written 3 months ago by DVA480 • updated 3 months ago by b.nota4.9k
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GSEA Phenotype Table Input
... Hello All, I am trying use GSEA for gene enrichment analysis, and I was wondering about the phenotype labels. Is there a way to test for the difference between two phenotypes while controlling for other phenotypes in a different category? For example, if I wanted to compare 5 cancer samples to 5 ...
gsea written 3 months ago by DVA480 • updated 3 months ago by c.chakraborty90
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Multiple factors & batch effects - DESeq2
... I have a question about how DEseq2 handles batch effects/ multiple factors. This is covered in the manual, but I just want to be certain I am doing it correctly. Say I have an experiment with this design: Sample Age Sex 1 Young F 2 Young F 3 Old F 4 Old F 5 Old F 6 Ol ...
deseq2 written 3 months ago by DVA480
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Comment: C: Horizontal lines in MA plot (DESeq2)
... Hi Kevin, Thank you for the reply. I think I kinda figured it out. Basically, it is described here: https://support.bioconductor.org/p/62927/ For every gene (row) DeSeq2 does a plus 1, to avoid 0 counts. Then it normalizes all samples based on the total count of each sample, and that gives a size ...
written 4 months ago by DVA480

Latest awards to DVA

Popular Question 15 days ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Voter 6 months ago, voted more than 100 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 8 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 8 months ago, created a question with more than 1,000 views. For Manually edit the flags in a sam file
Popular Question 9 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Centurion 9 months ago, created 100 posts.
Popular Question 13 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 13 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 13 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 14 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Popular Question 15 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 18 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 19 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 20 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 20 months ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
Student 20 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 22 months ago, created a question with more than 1,000 views. For Identify point mutations from each read in sam files
Student 22 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Student 2.3 years ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Scholar 2.4 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Illumina's HiSeq strange Phred quality score
Scholar 2.5 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Supporter 2.5 years ago, voted at least 25 times.
Scholar 2.6 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?

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