User: mahnazkiani

gravatar for mahnazkiani
mahnazkiani40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
4 years, 1 month ago
Email:
m**********@gmail.com

Posts by mahnazkiani

<prev • 19 results • page 1 of 2 • next >
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Tophat running error
... Hello, I'm trying to run tophat and I'm getting the following error that I don't know how to fix it. Appreciate any help. [2018-05-11 11:14:58] Checking for Bowtie Bowtie version: 2.2.9.0 [2018-05-11 11:14:58] Checking for Bowtie index files (genome).. [201 ...
tophat rna-seq written 6 weeks ago by mahnazkiani40 • updated 6 weeks ago by genomax49k
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Finding ortholog genes
... I have a question, I need to find the ortholog genes for the gene list that I have for the sorghum. I have my gene list, annotation file for sorghum that can be used for finding the arabidopsis orthologs and also zea_mays annaotation file that can be used next for finding the ortologs of arabidopsi ...
R rna-seq written 7 months ago by mahnazkiani40 • updated 7 months ago by yamule180
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De novo assembly and marker development for insecticide resistance
... Hello, I have a question for designing the experiment, I am interested to design markers for insecticide resistance in an insect that its genome has not been sequenced. I am thinking to sequence the genome, do de novo assembly and then look for variants between tolerant and control insect. Is this ...
next-gen sequencing written 9 months ago by mahnazkiani40 • updated 9 months ago by h.mon15k
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Comment: C: Differential Gene expression analysis with two factors
... Just wondering that does it makes sense to get DEGs from two genotypes and then use venn diagram to find similar DEGs in two genotypes and go through functional analysis after that? ...
written 9 months ago by mahnazkiani40
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Differential Gene expression analysis with two factors
... Hi, I have a question about RNA-seq data analysis, I have two genotypes and 3 sampling from a different part of the plant in each genotype. I want to analyze both genotypes together using factor analysis with a genotype: stage interaction term. How I can do that? Can I use edgeR? Appreciate your h ...
rna-seq written 9 months ago by mahnazkiani40 • updated 9 months ago by Devon Ryan81k
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Comment: C: Designing the RNA-seq for plant-insect interaction
... Thank you for your comment, I have two plant genotypes, one is resistant to insect and the other one is susceptible, I want to compare the gene expression of those two plants. The plants in the pots should be uniform because they are hybrid seed. Do you still think that is better to not have techni ...
written 12 months ago by mahnazkiani40
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Designing the RNA-seq for plant-insect interaction
... Hi, I am going to design a RNA-seq plant-insect interaction. I am not sure about how I should have biological and technical reps. If I collect the samples from 3 plants that planted in the same pot, can I consider each of them as technical reps and the whole pot as one biological rep and then the s ...
biological reps technical reps rna-seq written 12 months ago by mahnazkiani40 • updated 12 months ago by WouterDeCoster29k
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RNA-seq results comparison possible or not?
... I have 2 sets of data for my plant, the first set included 3 biological reps from plants that grown in 3 different times and got the samples from 2 parts of the stem to compare cell wall genes expression, my second set of plants grown in different light condition but still have 2 biological reps. ...
rna-seq written 24 months ago by mahnazkiani40 • updated 23 months ago by Biostar ♦♦ 20
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EdgeR output normalization?
... I have mean count output data from 3 biological reps that I got from edgeR implanted in CLC, I'm interested to do network analysis using these mean count data, do I need to do normalization before that or they are already normalized with CalcNormFactors-method-TMM?   Thanks       ...
rna-seq written 3.1 years ago by mahnazkiani40
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Network analysis-next step after calculating correlation in R
... I went through the R script that was online from the http://www.pb.ethz.ch/downloads/ . ############################################################################################################### # t_GCN.r script for computing targeted gene co-expression networks                               ...
R rna-seq written 3.2 years ago by mahnazkiani40 • updated 3.2 years ago by Jean-Karim Heriche15k

Latest awards to mahnazkiani

Popular Question 7 months ago, created a question with more than 1,000 views. For Network analysis-next step after calculating correlation in R
Student 7 months ago, asked a question with at least 3 up-votes. For Network analysis software
Popular Question 8 months ago, created a question with more than 1,000 views. For Network analysis-next step after calculating correlation in R
Popular Question 20 months ago, created a question with more than 1,000 views. For Network analysis-next step after calculating correlation in R
Popular Question 20 months ago, created a question with more than 1,000 views. For Do or not doing the Co-expression data analysis?
Popular Question 20 months ago, created a question with more than 1,000 views. For Network analysis software
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Network analysis software

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