User: tarek.mohamed

gravatar for tarek.mohamed
tarek.mohamed130
Reputation:
130
Status:
Trusted
Location:
Last seen:
1 week, 2 days ago
Joined:
2 years, 4 months ago
Email:
t************@northwestern.edu

Posts by tarek.mohamed

<prev • 80 results • page 1 of 8 • next >
0
votes
0
answers
109
views
0
answers
using tximport to prepare salmon quantification files for DEG analysis
... 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 ...
tximport rna-seq written 20 days ago by tarek.mohamed130 • updated 19 days ago by h.mon14k
0
votes
1
answer
233
views
1
answer
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 5 months ago by tarek.mohamed130 • updated 5 months ago by Hussain Ather860
0
votes
1
answer
562
views
1
answers
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.mohamed130
0
votes
1
answer
562
views
1
answers
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.mohamed130
1
vote
1
answer
562
views
1
answer
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 6 months ago by tarek.mohamed130 • updated 6 months ago by Kevin Blighe19k
0
votes
1
answer
359
views
1
answers
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.mohamed130
0
votes
1
answer
91
views
1
answers
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 6 months ago by tarek.mohamed130
0
votes
2
answers
335
views
2
answers
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 7 months ago by tarek.mohamed130
0
votes
2
answers
335
views
2
answers
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 7 months ago by tarek.mohamed130
1
vote
1
answer
463
views
1
answers
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.mohamed130

Latest awards to tarek.mohamed

Popular Question 16 days ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Scholar 5 months ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: efetch error LWP::Protocol::https not installed
Scholar 7 months ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Popular Question 19 months ago, created a question with more than 1,000 views. For installation of package 'rmarkdown' had non-zero exit status

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 986 users visited in the last hour