User: Manoj

gravatar for Manoj
Manoj80
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Posts by Manoj

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Comment: C: Quantifying abundances of transcripts using kallisto
... I figured out the updates. Here is my updated script: However, the genes in differential gene expression are very few numbers. names(files) <- paste0("sample", 1:187) txi.kallisto <- tximport(files, type = "kallisto", txOut = TRUE) head(txi.kallisto$counts) sampleMetaData < ...
written 8 weeks ago by Manoj80
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Comment: C: Quantifying abundances of transcripts using kallisto
... Yes! I am using tximport. Here is my script: However, the issue here is that my samples number are not equal so I am not sure how to improve the script instead of using "each=93". Please suggest. names(files) <- paste0("sample", 1:187) txi.kallisto <- tximport(files, type = "kallisto ...
written 8 weeks ago by Manoj80
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Comment: C: Quantifying abundances of transcripts using kallisto
... Hi, I am new in this analysis. I ran the kallisto and got all .tsv files then I merged these all files to make a single matrix file. It looks like this: Therefore, you mean I do not need to do differential expression analysis with this data, if so how I can use these data for RNA-seq analysis. Than ...
written 8 weeks ago by Manoj80
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Quantifying abundances of transcripts using kallisto
... Hi, I am analyzing RNA-Seq data. I have 190 PE samples (control: male, female, mutant: male, female) and generated featureCount matrix. For the differential gene expression, I used deseq2 with adjusted 0.05 p-value. On the other hand, I used kallisto for quantifying abundances of transcripts with ...
next-gen kallisto rna-seq written 8 weeks ago by Manoj80 • updated 8 weeks ago by swbarnes29.4k
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Comment: C: How to run DESeq2 for multiple factors
... Hi, do you have an idea about my question as I mentioned below? Is there any command to access these all .h5 files in a variable (files)? ...
written 9 weeks ago by Manoj80
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Comment: C: How to do unsupervised clustering of RNA-Seq data
... Hi, Thank you for your reply. I have made PCAs after transformation vsd and rld. But these seem mix-up all the samples. I need to make these in different groups to see the clear cluster. Please let me know if you have an idea. ...
written 9 weeks ago by Manoj80
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How to do unsupervised clustering of RNA-Seq data
... Hi, I have got count matrix of the RNA-Seq data (total 187 samples) using STAR and featureCounts. Here are the factors of the data: (affected: male and female and unaffected: male and female). And used DESeq2 package for DGE analysis. In the result, I have got 679 differential genes expressed with 0 ...
next-gen rna-seq clustering written 10 weeks ago by Manoj80
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Comment: C: How to run DESeq2 for multiple factors
... Here are some samples, in such a order I have total 187 samples: However, I am trying if I can access these samples by a single command. files <- c("/DataAnalysis/kallisto_test/270-aligned/abundance.h5", "/DataAnalysis/kallisto_test/272-aligned/abundance.h5", "/DataAnalysis/kallisto ...
written 11 weeks ago by Manoj80
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Comment: C: How to run DESeq2 for multiple factors
... Hi, first I am not sure how to load all abundance.h5 files from different folders. I have a total of 187 abundance.h5 samples files in different folders. files <- file.path(dir, "kallisto", samples$run, "abundance.h5") ERROR: Error in samples$run : object of type 'closure' is not subset ...
written 11 weeks ago by Manoj80
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How to make a PCA plot in three dimensional-RNA-Seq analysis
... Hi, I have 187 samples with two factors: (affected and unaffected) and (male and female) for RNA-Seq data analysis. I am using DESeq2 for DGE analysis. Therefore, I am trying to make a PCA plot to make different groups in three dimensional. I have tried to make a PCA here . However, I need to make i ...
next-gen pca rna-seq written 11 weeks ago by Manoj80

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