User: tarek.mohamed
tarek.mohamed • 130
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Posts by tarek.mohamed
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... Hi All,
I am using tximport to prepare quant.sf files generated from salmon for Deseq2 DEG analysis.
My quant.sf and txgenes files looks fine. However I got a message telling me that I have 3468transcripts missing from tx2gene.
I attached the code for tx2gene object generation.
What is causing this ...
written 20 days ago by
tarek.mohamed • 130
• updated
19 days ago by
h.mon ♦ 14k
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... 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 ...
written 5 months ago by
tarek.mohamed • 130
• updated
5 months ago by
Hussain Ather • 860
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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 5 months ago by
tarek.mohamed • 130
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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 6 months ago by
tarek.mohamed • 130
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... 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' ...
written 6 months ago by
tarek.mohamed • 130
• updated
6 months ago by
Kevin Blighe ♦ 19k
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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 6 months ago by
tarek.mohamed • 130
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... 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 6 months ago by
tarek.mohamed • 130
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... Also if you prefer to use R, you can use "Rsubread" package to count your reads using featureCounts () as mention by glihm.
T ...
written 7 months ago by
tarek.mohamed • 130
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... 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 7 months ago by
tarek.mohamed • 130
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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 7 months ago by
tarek.mohamed • 130
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For study power / sample size estimation for GWAS
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For A: Converting numeric to alphanumeric allele codes
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For C: efetch error LWP::Protocol::https not installed
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For A: Converting numeric to alphanumeric allele codes
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For installation of package 'rmarkdown' had non-zero exit status
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