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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Kallisto RNA-seq errors because of incompatible indices when running <kallisto quant> using downloaded mouse index
I'm trying to run RNA-seq on single-end mouse RNA data (50bp reads) but have very limited RAM (<4 gb) - I don't think I really have a way to work around this memory restriction, and wanted to try ...
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issue with rna seq analysis
I am working on RNA seq analysis and I would like to know the following things:
Current Methods:
downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38
performed ...
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Mitochondrial genes - TPM calculation bulk RNA-Seq
This question was also asked on Biostars
I was wondering if any of you have encountered a situation for bulk RNA-Seq where, possibly due to low sample quality or presence of dead cells, mitochondrial ...
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How to incorporate negative controls in DESeq2
We are doing a comparison between two outcomes (positive and negative). We could not have any positive controls as we do not have any "control" data to set as baseline, either from ...
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how to use CIBERSORT
I have seen in several articles, the use of CIBERSORT to calculate the proportion of immune system cells using gene expression data, I would like to try it but I have not found how to install it for R,...
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HISAT2: RNA strandedness
My library is unstranded and the code I'm trying to use is this:
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Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated
I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested ...
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how to install cibersort in R, to do deconvolution using my RNA-seq Data with public single cell data
I have RNA-seq Data from lung cancer immunotherapy patients but i don't have any single cell data from my sample, so i wanted to do a deconvolution with a public single cell data. I thought of doing ...
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Discrepancy with featurecounts analysis using a forward stranded and reverse stranded protocol
My RNAseq analysis pipeline is as follows: fastqc (read quality is good, some overrepresentation of adaptor sequence) → trimmomatic (trimmed adaptor sequence, qc report after trimming suggests the ...
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Cannot obtain alignment summary after running Bowtie2
I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:
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Working with Smart-seq3 data, have some questions regarding UMI and bar coding
Most of my experience has been working with genomic data, this time I am working on data from Smart-seq3. RNA excreted by cells in culture medium were processed with Smart-seq3 (From the looks of it, ...
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Question about umap using different numbers of pca components as initialization
I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different numbers of PCA components for initialization. The process involves projecting scRNA-seq ...
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scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?
I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search of dimensionality reduction/clustering parameters/methods. Some examples results I'm getting with ...
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Paired end reads with different read lengths
I downloaded some raw RNA-seq reads from NCBI using the sra-toolkit (Accession numbers: SRR2053159-64). The reads were generated using ABI SOLiD, and in colour space. I downloaded them in base space ...
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Using CSV files continaing scRNA-seq count data from GEO [closed]
I'm completely new to scRNA-seq analysis (and to most of Bioinformatics as well) so I apologize if this was asked a million times before.
I am trying to get the single cell expression data of lymph ...
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What are the output files of RNA-Seq from facility?
This question was also asked on Reddit
I am new in our lab and I am going to do bulk RNA-Seq. What type of files will we get from the company (Genewiz)? Will it be a bunch of Fastq files? or they give ...
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Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions?
Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions?
Regarding code, preferably using Python or R.
EDIT: Added a picture of the non-...
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Applying glmnet to identify predictors for subtypes
I am new to glmnet and other ML techniques, so apologise in advance if this sounds a trivial question. However, your guidance is very much appreciated.
So, I have nearly 700 genes with their ...
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Issue with Differential Gene expression analysis with Deseq2
I am using the Deseq2 package to perform a DE analysis on multiple factors.
So, basically to perform the analysis I consider patients characterized by the Brugada Syndrome type 1 and other patients ...
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DE analysis tool and method for non-coding features
I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the three DE test methods in edgeR such as ...
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Feasible to find genetic variations of two samples using RNAseq data?
I have bulk RNAseq data from two strains of mice from Jackson Lab: C57BL/6 and B6.SJL.
The former expresses a Ptprc-b allele and the latter expresses a ...
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is it possible to count cell in Violin plot in seurat?
I tried to quantify the number of cells of Fzd9+ Macrophage.
how can I know the cell count?
thank you
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Filtering criteria for non-coding features with very low counts
I am trying to do DE analysis of non-coding features of A. thaliana. I find in the miRNA and lncRNA counts file that they are abundant in zero counts, and most of the non-zero counts are very low. Now,...
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Statistical methods suitable for DE analysis of non coding RNAs
I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR package.
Is the negative binomial method that is ...
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building custom gtf file with entrez ID for any organism
How do I generate a custom gtf file format for a organism of my interest similar to human gtf file, in the custom gtf file I want to add entrez id to the new custom gtf.
My organism is ...
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Gene Expression Database for Psychological Disorders
Is there a comprehensive database available online of gene expression across the brain taken from individuals with psychological conditions? Resources like the Allen Institute's Human Brain Map (link ...
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Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs
I am writing to you to take an input or may be you can provide a different perspective. I am at wits end :(
So I have nearly 200 samples. These are separated into two groups (group I treated with ...
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Looking for datasets of RNA-Seq (or scRNA-Seq) for L1 larvae C. elegans
I was wondering if anyone know of a repository for C. elegans data sets, specifically in L1 larvae stage.
Are there any papers or GEO-sets for this organism at this stage?
thanks
Assa
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Integrate bulk RNA and ATAC-seq genes
I have up and down-regulated genes from bulk RNA result from DeSeq2. Genes that are differential in chromatin accessibility between two conditions from DiffBind. I would like to find the genes overlap ...
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What do the numbers mean in these RNA-Seq gene/transcript TPM files?
From the link https://gtexportal.org/home/datasets, under V7, I'm trying to do R/Python analyses on the Gene TPM and Transcript TPM files. But in these files (and to open them I had to use Universal ...
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Getting VCF file that contain common SNPs from 6 VCF file using isec
I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all the 6 files. I have tried this command
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How can I delete these lines in my fastq file?
Hi guys =) I'm sorry if this is a repeat but I haven't been able to find an answer using the search field or google.
I am trying to edit a fastq file that has a corrupt line. The read in question is ...
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What statistical test to apply for DE after CibersortX deconvolution?
This question was also asked on Biostars
I am running CibersortX in high-resolution mode (which yields estimates of gene values per sample).
After that, I want to perform DE between two conditions on ...
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Salmon Pseudo count when dealing with male and female RNA-seq data
I've generated a quant seq data that I intend to use to compare male and female gene expresion, with a focus on sexual chromosome.
For my species (three-spined stickleback), it is a classic XY sex ...
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Gene rank scores from LINCS database: Evangelista et al. 2022
The website https://maayanlab.cloud/sigcom-lincs/#/SignatureSearch/UpDown can be used to "Identify reversers and mimickers from over 1 million signatures by entering up and down gene sets .. &...
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How to use hashsolo for demultiplexing hashtags?
I am trying to use hashsolo and I want to make sure that I have done things correctly.
I did the below:
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Why is there antisense sequence in RNAseq data
I'm looking at RNAseq data from CCLE. The data is paired-end.
Take the cell line Hs578T and the gene HRAS as an example.
The cell line carries a G12D mutation (c.35G>A), so the change in cds is:
<...
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Integrating bulk RNA-Seq data with different sequencing depths and from different sources
I am attempting to integrate different bulk RNA-Seq datasets. While this is not ideal, I'm trying to reduce the technical variability in these datasets by using data generated by similar protocols (...
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Test for differences between groups of samples
Sorry if the answer to this should be obvious.
I have RNA-expression results from 24 samples which can be divided into 6 groups, (wildtype and two different mutants at two different ages) with a total ...
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How to remove orig ident. already data normalized, scaled assigned cluster/
How to remove orig ident. already data normalized, scaled assigned cluster/ Example, I have 4 sample data. like 1-control, 2- treatment with A, 3- treatment with B, and 4- treatment with C,
I want to ...
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How to differentiate DNA fastq and RNA fastq files?
I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains RNAseq data. But both have the RNA in the name but a different ID. How do I ...
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RNAseq alignment: best practices for aligning to multiple isoforms?
I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions.
Many of my (de novo assembled and ...
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How would you define a set of active genes from a bulk RNA-seq experiment in one biological sample? [duplicate]
I am trying to identify genes that are overall considered to be "actively transcribed" in my cell line of interest for some downstream analysis.
What would the approach be for defining this ...
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Nextflow Error: failed to read header from "-"
I am trying to run my nextflow pipeline, and have gotten this error:
samtools sort: failed to read header from "-"
I'm not sure why this error is ...
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RNAseq: Why would using a more complete scaffold reduce DEGs?
I have a set of RNAseq data for a couple of relatively under-studied species.
They're fungi, of the order Hypocreales. The assemblies we're working with are de novo - reference seqs don't actually ...
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Generating gene signature for sample classification and survival analysis patient cohort
This is from this paper
The LSC17 score is calculated for each patient as a linear combination of GE of these 17 genes weighted by regression coefficients that were estimated from the training data as ...
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Nextflow Pipeline: Unexpected Input "{"
I'm attempting to run a nextflow pipeline and have begun getting unexpected output for a few of the processes in my pipeline. I believe this to be a syntax error, but I am not sure where to correct it....
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To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?
I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same ...
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Gene symbol list for all protein coding genes in mice
How can I get a csv or a list of the gene symbol names for all the protein coding genes in mice? I have RNA sequencing data and I'm not interested in the non-coding stuff. I'm worried it could mess ...
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Inconsistent replicate numbers in RNA-seq
I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake ...
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