User: DVA
DVA • 480
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Posts by DVA
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... Thanks for the help! Appreciate it. ...
written 2 days ago by
DVA • 480
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... Thank you for the comment @genomax, I am looking at individual base level. ...
written 4 days ago by
DVA • 480
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... 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. ...
written 4 days ago by
DVA • 480
• updated
4 days ago by
Pierre Lindenbaum ♦ 112k
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... 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 ...
written 10 weeks ago by
DVA • 480
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1
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155
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1
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... Thanks so much for the information! ...
written 3 months ago by
DVA • 480
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155
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1
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... 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 ...
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... 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 ...
written 3 months ago by
DVA • 480
• updated
3 months ago by
c.chakraborty • 90
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... 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 ...
written 3 months ago by
DVA • 480
0
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297
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... 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
DVA • 480
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For Non-cancer somatic mutation calling
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