User: Manoj

gravatar for Manoj
Manoj80
Reputation:
80
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United States
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14 hours ago
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5 years, 5 months ago
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Posts by Manoj

<prev • 193 results • page 1 of 20 • next >
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Comment: C: DESeq2 analysis with high number of samples
... I think it is understandable not to be able to show differential gene expression with a high number of samples since these are randomly picked (mix of samples) from the patients and normal. Yes! I would run all 200 samples and see. ...
written 1 day ago by Manoj80
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DESeq2 analysis with high number of samples
... Hi all, I am performing RNA Seq data analysis in order to identify differential gene expression analysis on a large number of samples (~200). Initially, I ran [STAR][1] with 40 samples (20 affected and 20 unaffected). I got a featureCount matrix. Now, I am performing DESeq2, but once I do the DEseq ...
next-gen deseq2 rna-seq written 1 day ago by Manoj80 • updated 1 day ago by RamRS30k
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Comment: C: How to do DESeq2 for Kallisto
... I did not know about it. If you could really want to help, you could have sent the link instead of commenting on me. I mentioned that I am new about the analysis and do not know about the coding either. ...
written 2 days ago by Manoj80
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Comment: C: How to run STAR with multiple files
... I did not get what is file01_R1.fastq_R1.fastq. Could you please clarify that? ...
written 2 days ago by Manoj80
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Comment: C: How to do DESeq2 for Kallisto
... However, I need one more help in the following code. What should I use here instead of ColData. vsd <- vst(dds) class(vsd) head(ColData(vsd)) plotPCA(vsd, "condition") ...
written 2 days ago by Manoj80
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Comment: C: How to do DESeq2 for Kallisto
... I got it! if I write with rep as following: sampleTable <- data.frame(condition = factor(rep(c("mutant", "control"), each = 18))) ...
written 2 days ago by Manoj80
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Comment: C: How to run STAR with multiple files
... I tried but not working. ...
written 2 days ago by Manoj80
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Comment: C: How to do DESeq2 for Kallisto
... I am not catching entirely. I am following the [tutorial][1] I am new in this analysis. I tried to change but not getting improved. If you could help me to improve the code. sampleTable <- data.frame(condition = factor(rep(c("mutant","mutant","mutant","mutant","mutant","mutant","mutant ...
written 2 days ago by Manoj80
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Comment: C: How to run STAR with multiple files
... I tried with or without a comma. However, it is showing the same error. Also, I tried with ls before raw_data. It is showing the following ERROR. ls: cannot access raw_data/270_R1.fastq,raw_data/270_R2.fastq: No such file or directory ls: cannot access raw_data/272_R1.fastq,raw_data/272_R2. ...
written 2 days ago by Manoj80
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Comment: C: How to run STAR with multiple files
... I have improved the script. However, it is still showing the following error. for i in $(raw_data/270_R1.fastq,raw_data/270_R2.fastq raw_data/272_R1.fastq,raw_data/272_R2.fastq raw_data/274_R1.fastq,raw_data/274_R2.fastq raw_data/278C_R1.fastq,raw_data/278C_R2.fastq raw_data/284C_R1.f ...
written 2 days ago by Manoj80

Latest awards to Manoj

Great Question 3 months ago, created a question with more than 5,000 views. For how to run repeatmasker
Popular Question 4 months ago, created a question with more than 1,000 views. For rename files names in a directory based on list of names
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Centurion 12 months ago, created 100 posts.
Popular Question 4.8 years ago, created a question with more than 1,000 views. For rename files names in a directory based on list of names
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Popular Question 4.8 years ago, created a question with more than 1,000 views. For remove duplicated entries from BLAST result file
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