User: tarek.mohamed

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tarek.mohamed130
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Posts by tarek.mohamed

<prev • 79 results • page 1 of 8 • next >
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Plotting linkage equilibrium results
... Hi All , I did a LD analysis using a combination of bedtools, vcftools, and plink. I had 9000 SNPs distributed across 4 different genes which I did LD analysis for. Now I have LD analysis result (plink.ld) file. I want to view the analysis graphically, which tool do you recommend? [tmm447@qu ...
plotting ld heatmap linkage disequilibrium plink written 9 weeks ago by tarek.mohamed130 • updated 9 weeks ago by Hussain Ather700
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Comment: C: linkage disequilibrium analysis
... Hi Kevin , I was able to do the analysis using a combination of bedtools, vcftools, and plink. I had 9000 SNPs distributed across 4 different genes which I did LD analysis for. Now I have LD analysis result (plink.ld) file. I want to view the analysis graphically, which tool do you recommend? ...
written 9 weeks ago by tarek.mohamed130
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Comment: C: linkage disequilibrium analysis
... Hi Kevin, Thanks for your reply. Actually, I tried vcftools, but I got negative values for r2 which of course does not make sense! I am going try the long way approach, and I will let you know the updates. Thanks, T ...
written 3 months ago by tarek.mohamed130
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linkage disequilibrium analysis
... Hi All, Using 1000 genomes database, I have downloaded genotype data for 99 individuals for couple of thousands of SNPs distributed across different chromosomes, I have this data in one vcf file. I want to perform linkage disequilibrium analysis between all of these SNPs, I need the r2 and the d' ...
different chromosomes snps ld written 3 months ago by tarek.mohamed130 • updated 3 months ago by Kevin Blighe12k
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Answer: A: SNPs and Gene Expression
... Hi, Are you trying to do an eqtl? ie. investigate which snps are associated with alteration in genes expression. T ...
written 3 months ago by tarek.mohamed130
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Answer: A: DiffBind DESeq2 for multiple comparisons
... Hi, You can do this using deseq2 by modifying the deseq2 design in a way that fits your need. Please have a look at this discusion https://www.biostars.org/p/278684/#278695 T ...
written 4 months ago by tarek.mohamed130
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Comment: C: counting the reads that mapped to a part of transcriptome
... Also if you prefer to use R, you can use "Rsubread" package to count your reads using featureCounts () as mention by glihm. T ...
written 4 months ago by tarek.mohamed130
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Answer: A: counting the reads that mapped to a part of transcriptome
... Hi Sara, Did you align the raw reads to a reference genome? if so what is the current format of your aligned reads? Tarek ...
written 4 months ago by tarek.mohamed130
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Comment: C: How is the design in DESeq2 work?
... Regarding 'design = ~Strain + Time + Strain:Time` , Here you added an interaction term (how time is interacting with stain in relation to regulation of gene expression). So this design will return the effect of time on the reference level of strain (1 or 2 depends on your setting). Using contrast ( ...
written 4 months ago by tarek.mohamed130
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Comment: C: How is the design in DESeq2 work?
... Hey, To the best of my knockledge A) `design = ~Strain + Time` means that deseq2 will test the effect of the Time (the last factor), controlling for the effect of Strain (the fi rst factor), so that the algorithm returns the fold change result only from the effect of time. B) `design = ~Time` here ...
written 4 months ago by tarek.mohamed130

Latest awards to tarek.mohamed

Scholar 12 weeks ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For C: efetch error LWP::Protocol::https not installed
Scholar 4 months ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Popular Question 16 months ago, created a question with more than 1,000 views. For installation of package 'rmarkdown' had non-zero exit status

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