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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 (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.

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Is there a method to write one ambiguous rna sequence from multiple unambiguous rna sequences in Python 3?

I have many rna sequences of the same length. Now i want to create a function that will give me one line of ambiguous rna as output. So far i'm not finding any useful information on writing ambiguous sequences online. I thought about using a…
mavi123
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rMATS error "unable to access a shared library"

I am trying to run rMATS on a Linux (CentOS) cluster. On this system I do not have root access. I installed several of the rMATS dependency packages using the anaconda conda install package manager. rMATS is unable to access a shared library…
Paul
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Error on Google Cloud - Genomics: "API solution not found with service name: genomics"

I am completely new to the HPC and Google Cloud (I just signed for a trial account) . My Idea is to perform a RNAseq analysis (9 samples paired, 18 fastQ files), Mainly I want to perform the FastQC and the mapping trying different aligments.…
FJ_Bioinf
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ERROR when trying to run Nextflow for RNAseq on MacOSX (M2)

The error I am getting is this right when I try to download the pipeline and test it on a minimal dataset with a single command: $ nextflow run nf-core/rnaseq -profile test,conda --outdir /Users/aggardik/workflow N E X T F L O W \~ version…
Angeliki
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Why do I keep getting an error for index length when I try to build a Cytoscape enrichment map from GSEA data?

I am new to Cytoscape and GSEA, but am trying to build an enrichment map with my RNA-seq data. I have uploaded the .gmt file and two .xls files, one for positive enrichment and one for negative. I also have a .rnk file but that doesn't seem to be…
KBO
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Is there a way to calculate the Z score for all values in a row in a data frame?

I have a data frame which contains expression levels of a gene in 1677 conditions. I am looking to create a new data frame which has the Z score for each condition. This is the code I have so far: for (cell_no in 1:ncol(NANOG_data)) { …
menan
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Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical

I am running RNA Seq analysis on a dataset and I keep receiving this error when using DESeqDataSetFromMatrix. The df is counts data and the coldata is coldata. Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be…
Skylar Gay
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How do I filter the rows in a data frame by condition in R

I am working on 4C data where I have a .txt file that contains chromosome, start,end, nReads, RPMs, p.value, q.value and I am only interested in significant interactions in chr15 and later want to filter the interactions that are farther than 100kb…
koushik ayaluri
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for-loop linear regression generation new dataframe with the results

I want to write a loop on R to perform linear regression on my dataset genes (= 210011 genes and 6 samples total; with columns the gene and the rows the samples) to identify how age and sex affect gene expression. I want to save the fitted value…
cb_1990
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How to make all lines in count plot start from the control group

I am trying to make a count plot from RNA-seq data for individual genes. I am only interested in the comparisons between each treatment and the control group and my data are paired, so I'm trying to show this. I have managed to make the graph on the…
AndreaWall
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Extracting read counts matched to each gene symbol

I have quantified gene expression by Salmon that gives me Ensembl transcripts, I converted Ensembl transcripts to gene symbol but for some genes I multiple transcripts; How I could collapse read counts to genes, I tried tximport package but I found…
Angel
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Error Pegasus package: TypeError: highly_variable_features() got an unexpected keyword argument 'consider_batch'

I am using Pagesus package to analyze my single cell RNA sequencing data. I have encountered the following error using the Pegasus package for single cell analysis. The function that is giving me the error seems to be: highly_variable_features(data,…
FVG
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