User: tarek.mohamed

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tarek.mohamed110
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t************@northwestern.edu

Posts by tarek.mohamed

<prev • 77 results • page 1 of 8 • next >
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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 days ago by tarek.mohamed110
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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 days ago by tarek.mohamed110 • updated 3 days ago by Kevin Blighe7.3k
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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 4 weeks ago by tarek.mohamed110
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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 weeks ago by tarek.mohamed110
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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 5 weeks ago by tarek.mohamed110
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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 5 weeks ago by tarek.mohamed110
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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 5 weeks ago by tarek.mohamed110
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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 5 weeks ago by tarek.mohamed110
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Answer: A: How to start analyzing next-generation DNA and RNA sequencing data?
... Hi Ben, Do you want to exclusively use R, or you are up to other unix-based tools as well? T ...
written 5 weeks ago by tarek.mohamed110
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Comment: C: PLINK2 recode ped flag issue
... What do you mean by REF alleles are incorrectly assigned. Can you attach an example. T ...
written 7 weeks ago by tarek.mohamed110

Latest awards to tarek.mohamed

Scholar 7 weeks ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Popular Question 13 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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