User: monaallouba

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Posts by monaallouba

<prev • 12 results • page 1 of 2 • next >
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Comment: C: power analysis and rare variants
... allele frequency in a control population so basically, I am trying to address the following question: At what control cohort size will I have 80% statistical power (with alpha = 0.05) to detect very low frequency variants (i.e. 0.001)? ...
written 3 days ago by monaallouba0
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power analysis and rare variants
... Hello, I need to assess how many individuals I need to sequence to find all variants with an allele frequency <0.001 with a power of 80%. How can I do that in R? Thank you ...
power analysis rare variants written 3 days ago by monaallouba0
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failure to run merlin parametric linkage analysis
... Hello, I have converted my plink files into merlin via mega2. I then tried to run the basis parametric linkage command merlin -d parametric.dat -p parametric.ped -m parametric.map --model parametric.model --step 3. But I get the following error: FATAL ERROR - Error reading named allele frequencie ...
merlin mega2 linkage analysis plink written 7 months ago by monaallouba0
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remove singletons in LD pruning in plink
... Hello, How can I remove singletons in LD pruning in plink?Is there a specific command for that? Thanks ...
singletons plink ld pruning written 7 months ago by monaallouba0 • updated 7 months ago by chrchang5236.9k
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Comment: C: haplotype analysis - softwares
... Thanks Kevin. So the thing is that I have identified a specific mutation that is prevalent among my disease cohort but is absent in controls. I would like to assess two things: 1. If the mutation segregates with the disease in affected families 2. If the mutation lies in a haplotype that is shared ...
written 7 months ago by monaallouba0
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haplotype analysis - softwares
... what is the best program to use if I want to assess whether a specific mutation lies in a haplotype that is shared among all mutation-carriers? ...
software haplotype written 7 months ago by monaallouba0 • updated 7 months ago by Kevin Blighe60k
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power analysis for gene burden test
... Hello, How do I perform a simulated power calculation for gene burden testing in R whereby I predict the frequency of variation in controls to be 1% and then show the change in power for a given gene burden at differing sample sizes? Thank you ...
power burden R written 8 months ago by monaallouba0
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Comment: C: Allele specific expression
... no targeted sequencing ...
written 10 months ago by monaallouba0
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ref and alt allele count from BAM file
... Hi All, I would like to calculate the allele ratio of ref/alt at a specific position. How can I determine the ref and alt counts from the BAM file? (or is it better to extract this info from the VCF?) Thank you ...
bam allele_count rna-seq written 11 months ago by monaallouba0 • updated 11 months ago by Vitis2.3k
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Comment: A: Allele specific expression
... Thank you very much for your response @geek_y :) The problem now is that my BAM file shows the the ref and alt reads but this site is completely absent in the VCF :/..Any ideas how I can resolve that? or can I just determine the number of ref and alt reads from the BAM file? ...
written 11 months ago by monaallouba0

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