Questions tagged [rna-seq]
RNA-Seq (named as an abbreviation of "RNA sequencing") is a technology-based sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome.
rna-seq
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Add QC matrices to the seurat object while working with scRNAseq data
I am trying to analysis scRNAseq data and have both matrix and h5 as input for my pipeline (I have tried both off them). I have used the same pipeline before and worked perfectly.
the following lines ...
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using PCA to filter outliers in MATLAB
A bit of a silly question (I suspect). I am using MATLAB to preprocess some bulk RNAseq data. I am calling PCA on my normalized counts just as an initial way to identify outliers I didn't ...
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RNAseq sequence alignment
When I have my RNA sequences and I am going to map them to the reference genome, should I use both haplotypes, use only one, should it be haplotype A?
Could you share some reasons why and or some ...
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DESeq 2 error: Error in checkFullRank(modelMatrix) : the model matrix is not full rank
I'm trying account for two sources of variation when I did PCA in my data set. The two conditions look like this:
My table
My code:
data_matrix <-fread("/Users/claireweaver/Data/SRA/...
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Rule Exception: Called Process Error Snakemake pipeline
I'm attempting to run the SPLINTR barcode seq pipeline on the test fastq files.
https://atlassian.petermac.org.au/bitbucket/projects/DAW/repos/splintr_barcode_seq_pipeline/browse
My Conda environment ...
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Importing RNA seq raw counts as nsorted.htseq.counts files in R
I have a list of RNAseq raw counts data (one file for each sample) in directory with extension nsorted.htseq.counts. I would like to import all of them and to combine in one dataset. How can I do it?
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
I am new to RNAseq and started to analyze my dataset using DESeq2. I first run the DESeqDataSetFromMatrix function and found the error message Error in DESeqDataSetFromMatrix(countData = HitCount, ...
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IsoformSwitchAnalyzeR in R
I want to find isoform switches for a disease and I have the RNASeq expression data file (it's a CSV file with info about the 2 stages I want to compare and study). The RNASeq was done using Kallisto. ...
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GOcircle function in GOplot not plotting correctly
I'm trying to create a GO circle figure for my bulk RNAseq data. I ran the original RNAseq analysis in R using DESeq2, and enrichGO for performing GO analysis.
I'm having difficulty with the GOplot ...
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doing some ontology enrichment analysis
I have my RNA sequencing results output from DeSEQ2 and eager to generate some figures. I try to run the following command, only for it to tell me that the input does not match the required format, ...
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How do I pull down single cell RNA sequencing data from NCBI and process with python?
I am new to scRNA sequencing analysis and having a hard time beginning the process of data analysis. I'm downloading the roughly 35GB dataset from NCBI using SRA ToolKit. (https://trace.ncbi.nlm.nih....
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My plots only show in a separate window. How can I undo this?
I am using RStudio and doing scRNA sequencing analysis. I am trying to plot my clusters and they keep pooping up in a new window called R Graphics: Device 2 (ACTIVE).
This is my code:
DimPlot(pbmc....
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DESeq object - how to correctly define the design statement
I'm trying to analyse RNAseq data using the DESeq package, however i am unsure on what the right design would be for my experimental setup.
I have three different treatments, where i am always ...
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DESeq2 issue: can't create DESeq2 object
I'm trying to analyse RNAseq data using the DESeq2 package in R, but I'm quite new to it. I'm running into an issue when I want to create the DESeqDataSheet. I keep getting the following error:
Error ...
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RNA Seq ggVennDiagram ERROR: `stat_sf()` requires the following missing aesthetics: geometry
I'm trying to create a 5 set Venn Diagram from a lists of lists of differentially expressed genes (after running DESeq2), and because the easy-to-use R packages allows up to 4 sets, I'm using a ...
