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Questions tagged [rna-seq]

Questions should include this tag if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design or transcriptome assembly...

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5 views

Matching these matrices in R

I have two matrices; I want to convert the row names of first matrix to gene symbol from matched ensemble=gene symbol from second matrix ...
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1answer
33 views

Finding genes especific to microenvironment

I have RNA-seq .bam files for 3 patients, tumour and its matched derived model, namely organoid, but I don't have any matched normal sample. Differentially expressed genes between a tumour and its ...
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1answer
59 views

Running htseq-count over BAM files

I am trying to derive an expression matrix from BAM files using htseq-count on the server. These are bulk RNASeq BAM's by the way. I have read the ...
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1answer
52 views

Assembly by stringtie

I run this cmd ./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4 -C G1.refs.gtf -A G1.abund.tab Error is: ...
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1answer
29 views

Error in formation of correlation matrix-(corrupt matrix — dims not not match length)

I am working on a script to create a correlation matrix and mutual_rank matrix from RNAseq gene counts for 57992 genes in 7027 samples. I have already tested this script for a smaller file (for 10,000 ...
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0answers
59 views

lower mapping rates in salmon v0.13 compared to previous versions

Hi there :) Thanks for the tool! I recently updated to the new salmon (from 0.8... its been a couple years) and I noticed that my mapping percentages change dramatically between the two versions. ...
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1answer
39 views

I need some tips and suggestions for further analysis of NGS expression data (log2cpm)

I am a PhD student who inherited some log2cpm data of expression data from bulk kidney tissue from a UUO(unilateral urethral obstruction) experiment that tests a new drug. The sample material consists ...
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1answer
50 views

Discordance in gene signature behavior between bulk and single-cell RNASeq

The objective of the following analysis is to identify an activation signature of a specific phenotype on bulk RNASeq and to apply it to single-cell RNA-Seq, in order to identify the population of ...
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1answer
10 views

Empty .result in MirDeep Star

I am using MirDeep star tool for RNA sequence alignment. I have tried both GUI version and command line version of this tool. But every time, I am getting empty . result file and .known_mir file. This ...
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0answers
57 views

Getting genes specially up or down regulated

I have 6 RNA-seq samples like this 4 patients (005, 036, 121, 013) I have 3 tumour samples and 3 cancer models (organoid) This is PCA of log transformed data by ...
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3answers
97 views

Normalization for two bulk RNA-Seq samples to enable reliable fold-change estimation between genes

I have two bulk RNA-Seq samples, already tpm-normalized. I would like to know what is a reasonable normalization procedure to enable downstream log fold-change estimation. The distribution of the ...
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0answers
28 views

What Ensembl genome version of wheat should I use for alignments? [duplicate]

There are many genome files available from Ensembl. Which one is the best to use/download for wheat RNA seq differential gene expression analysis? Also, tell me which tool or aligner or mapper to use? ...
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27 views

P21 mutant Colon Cancer cell lines (RNA SEQ)

I need to obtain RNA sequence datasets for my project. The datasets should include P21 mutation, knockout and wild type in any Colon Cancer cell lines, Preferably in the same study. I'm not sure if ...
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0answers
31 views

Making a bed file for RSeQC

I making a bed file for RSeQC, so it can do things like compute the number of reads from exons, introns, 5"UTRs, etc. I want to use a bed file that corresponds to my GTF file, so I use gtf2bed to ...
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1answer
45 views

Where to Download Cancer Raw Reads (fastq)?

Does anyone know where I can download cancer raw reads (fastq files), tumor and Germline for non-humans? I wanted to make a study with human data but I don't have the control access to download raw ...
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0answers
22 views

Common Mouse and human DEG analysis

I have DEGs from human and mouse (equivalent of a human disease model), and would like to generate a logCPM correlation plot between the overlapping mouse and human gene (275 genes). Prior to ...
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2answers
51 views

Using preprocessing/alignment functions on the server

I am new to bash and the processes behind cluster computing in general and need some help with understanding some basics. After looking all over the internet and this forum (+ askUbuntu) I found ...
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1answer
97 views

Error in as.vector(x) : no method for coercing this S4 class to a vector

I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error: <...
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2answers
32 views

Get & Annotation of isomiR (isoform of miRNA) profile from RNA-seq

I should get and analyse isomiR (isoform of miRNA) profile from RNA-seq with FASTA format. The best tool for this is "DeAnnIso". But here is a problem with this tool, it only allows you to upload ...
2
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1answer
15 views

RSeQC provided bedfile does not work with read_distribution.py

I frequently make use of RSeQC, I used to use it with my own bed file, generated using gtf2bed, but now I thought I'd use the one provided by RSeQC themselves from here, I got the file ...
2
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3answers
120 views

Question about Co-expression analysis and finding targets for lncRNAs

I have a dataset with 88 tumor and 113 normal samples. Among the 50k genes after filtering there are a total of 28k genes (both mRNAs and lncRNAs) I wanted to do co-expression analysis between ...
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1answer
34 views

RNA-seq gene/transcript read counts database for Mouse

Is there any RNAseq gene/transcript read count database for the mouse? I already know about ARCHS4, looking for some other source. Thank you
2
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1answer
54 views

How can I interpret gene expression data from Bioconductor packages?

I am currently looking at microarray data from a bioconductor microarray dataset. Specifically, I have data (a snippet) which looks like the following: ...
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1answer
58 views

How I know which gene is a good predictor in this neural network or not?

I have 25 highly differentially expressed genes among responder (TRG12) and non responder (TRG45) patients to chemotherapy. I have made a neural network of these genes. Accuracy of model is 0.73 but ...
2
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1answer
24 views

Pathway plot in GeneTrail data base

So I'm doing a pathway analysis using GeneTrail database. One thing I am not able to get is this similarity measure being calculated and plotted: I want to know how this is being made, what is the ...
2
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3answers
133 views

How to quantile normalization on RNA seq counts

I have a read count data (RNAseq) and want to perform quantile normalization. Could you please help me how to do it. I tried some scripts in R but it didn't work. I want the result output in matrix ...
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1answer
60 views

data storage requirements for RNA-seq and WGS

Supposing upcoming RNA-seq for 3 conditions and 3 replications for each, how much is data storage requirements?
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2answers
135 views

Extracting some part of a list

I have two normalized gene expression values (log2 of cpm) ...
1
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1answer
45 views

Calculating Z-score from logCPM values using edgeR

I have the raw counts for RNA-Seq data. I converted counts data to logCPM using edgeR package. Lets say I have a dataframe A with 15000 genes as rows and 100 ...
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0answers
62 views

Several models identify different which genes are significant

I want to find some good predictors (genes). This is my data, log transformed RNA-seq: ...
3
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1answer
91 views
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1answer
34 views

log rank p value interpretation from gepia 2

How do i interpret the overall survival when the p value reported is not significant going by the standard convention . Not sure what kind of test it runs while comparing the expression may be one ...
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1answer
82 views

Changing this function to work

I have this matrix of expression data ...
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1answer
53 views

how to write italic script in Rstudio [closed]

I have got the problem on how to write the italic script in RStudio. I used the script in the screenshot and got the error "Error in grobs[[i]]: subscript out of bounds."
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0answers
53 views

Making a model of gene contribution in cancer diagnosis

I have raw read counts (Edgeseq technology) of 56 patients who have been ranked with Mandard score as responders and non-responders; I have done differential expression by DESeq2 and I obtained a ...
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1answer
37 views

Extracting genes differentially expressed by Wilcox test

I have 2 cell types (NOF and CAF) cultures individually and also have been co-cultured with tumour like this picture. https://ibb.co/x8Ty1Wz If this is the log cpm of these 4 samples ...
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1answer
60 views

Experimental Design for Differential expreression analysis

I have a Normal esophageal Fibroblasts (NOFs) cultured in DMEM media; The same NOF also have been cultured with a tumor sample from a patient named 005 on DMEM media; I have also Cancer Associated ...
2
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1answer
45 views

sva for RNA-Seq data without known phenotype

I have been working on RNA-Seq data from two different cohorts, and they show very strong batch effect (~35% variance explained by 1st component in PCA). Since I am trying to do a class discovery from ...
2
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2answers
72 views

How can I extract the longest N isoforms per gene from a fasta file?

The question of how one can extract the longest isoform per gene from a multi-fasta file has been answered expertly in this thread: How can longest isoforms (per gene) be extracted from a FASTA file? ...
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0answers
38 views

Why are TPMs per 10k or 100k in many scRNA-seq studies?

I noticed that many scRNA-seq papers normalize TPMs to 10k or 100k as opposed to 1M (as the abbreviation defines them). It doesn't really matter since you are just moving the decimal point, so why ...
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1answer
76 views

Why is a PacBio read length larger than the aligned reference region?

I recently had some Iso-Seq sequencing done on my organism catfish on the new Sequel platform and got weird alignments for a size selected 4 Kilobase and up fraction after running the isoseq3 pipeline....
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2answers
55 views

How to link GDC ids to CCLE cell line names?

Hello bioinformaticians, I've recently downloaded few RNAseq data files from Genomic Data Commons Data (GDC) portal. These files belong to Broad institutes CCLE project. Now the problem is that GDC ...
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4answers
63 views

How to get the longest fasta sequence including all possible switching isoforms of a gene out of isoforms

I am working with RNA-seq data without a reference genome/transcriptome and am instead using a Trinity de novo transcriptome assembly. I analyzed both isoform and gene expression abundances using RSEM....
2
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1answer
26 views

Real time transcript profiles

Do any methods exist (or are in the process of development) for investigating transcript data without lysing the cells, i.e, destroying the sample?
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2answers
50 views

Why the t-test for a specific gene shows different value compared to differential analysis?

I have RNA-Seq data for LUNG cancer. 370 tumor and 50 Normal. For differential analysis initially I did some filtering and kept approx. 19k genes for further analysis. I used edgeR. With a FC > or &...
3
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1answer
47 views

How should I address batch effects in my experiment?

Let's say I have an RNA-Seq experiment, where I'm interested in the significantly differentiated genes between pre-treatment and post-treatment conditions. "rep" == biological replicate. ...
2
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1answer
47 views

Question about the dots on Quartile groups in boxplot

I have Microarray Normalized Expression data for a specific Gene. It looks like below in a dataframe B ...
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1answer
162 views

Integrative analysis of omics studies using machine learning

I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow: Normalise samples, within each type of omics, from ...
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0answers
115 views

GO Term heatmap plot in terms of P value or fold enrichment

I'm clustering genes in terms of expression after clustering them. I'm taking out clusters and trying to find out what kind of GO terms are coming up. I came across this figure from this paper, I want ...
1
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1answer
104 views

How to get the corrected matrix after SVA batch effect correction

I ran SVA to remove batch effects for my bulk RNAseq experiments, but now I need to somehow correct my data matrix in order to ...