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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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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How can I process fastqs generated using the inDrops protocol into a counts matrix?
Cross-posted on Biostars
I'm trying to re-analyse scRNA-seq data from a recently published manuscript. The methods state that the data was generated using the inDrops protocol, but doesn't mention ...
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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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Which candida albicans fasta and gff file should I use for alignment?
I downloaded the gff and fasta files for candida albicans from http://www.candidagenome.org. I want to use hisat2 to align some fastq files against it.
There are ...
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How to calculate cell type percentage in every sample
I have a Seurat object (metadata) with the single R samples consisting of cell types and sample types columns. I am trying to make a table that has a sample and percentage of cell types for each ...
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How much does Nanopore cDNA Sequencing Cost?
[this question is based on a question that was asked on Reddit]
We're interested in doing whole-transcriptome cDNA sequencing of 30 mouse cell lines, and are deciding between Illumina and Nanopore ...
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blood contamination rna seq
I have tumor rna seq samples. I want to find out percentage of blood contamination within these samples. What is the best possible way to find % of blood contamination within the rna seq samples?
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Error while using SummarizedExperiment() in R
I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data:
...
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Does the contrast matrix I have made address the question I am trying to answer?
I have the following design matrix:
mm_noreps.interactions <- model.matrix(~condition*TRAPed)
Both variables are factors condition has 4 levels and TRAPed has 2 ...
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Is it possible to do homology inference across species using different kinds of NGS data?
Background: I have a list of species that I want to put through homology inference. The goal of homology inference is to investigate the evolution of a trait on a species tree. I want to use the ...
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Examples of machine learning approaches to validate results where ground truth is lacking?
I am currently looking into some of the published methods for deconvolution of spatial transcriptomics data where each spot does not have single-cell resolution. These methods all rely on cell type ...
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Display row and column names in R
I have plotted a heat-map with 235 rows and 570 columns which is below: how do we make clear names of row and columns on this graph using R?
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Kallisto error: index input file could not be opened!
I am utilizing Kallisto in Anaconda/miniconda for RNA sequencing. I have successfully made ...
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How to remove double '/' from file path, bash script
I'm using the following script to detect strandedness of my paired end RNA-seq data.
...
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How to run how_are_we_stranded_here?
I'm trying to run the python library called how_are_we_stranded_here. I have installed with pip install how_are_we_stranded_here. I have also installed its ...
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How do I determine read length from a user-inputted fastq file and then input that information into a tool's command line?
Can you guide me on how could take an input fastq file, read the length from read and then feed it into the findtail's command?
I have suggested concerns about documentation and program defaults to my ...
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How to make unrooted tree for Likelihood mapping result by using IQ2-tree?
I am a biologist, and I do not fully understand the tree topology of the experimental species.
I used four-taxon set (4 sequences) to identify the Four-cluster Likelihood-Mapping by using
...
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What are the conditions to perform Gene Expression Analysis on data you've performed RNA Sequence Analysis on?
I want to perform Differential Gene Expression Analysis. I recently completed RNA Sequence Analysis using the Seraut Tutorial up to this point: Finding Differentially Expressed Features (Cluster ...
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Can I perform Expression Analysis on this 10x dataset?
10x Genomics: 20k Human PBMCs is the dataset.
Description of the dataset:
Inputs/Libraries
Human peripheral blood mononuclear cells (PBMCs) of a healthy male donor aged 30-35 were obtained by 10x ...
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Calling isoforms from long read data generated from partially degraded RNA
What will be the best tool to call isoforms from long read data generated from partially degraded RNA. By mistake we processed some samples with poor quality RNA to generate long read. Now we are ...
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How to find closely related genes for a specific gene from WGCNA modules?
I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by performed pathway analysis with the genes present in those modules.
Among all ...
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Benchmarking for variant identification using RNA-seq data
I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the ...
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Ubiquitous regulation of highly specific marker genes
I am fairly new to scRNAseq analysis and keep running into the same problem in the two datasets I am currently working with. We work with kidney inflammation and have two new mouse models, which we ...
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Snakemake MissingRuleException
I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message.
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Number of Spots in a Spatial Seurat object
I have got an integrated seurat object of 21 Spatial samples. I want to know how many spots are in all the samples together, Is there a way I can do that? Also, Please suggest any R Packages that do ...
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Stringtie/DEprep.py gene/transcript IDs are wrongly formatted
Hi my RNAseq workflow is ending up with wrongly formatted gene IDs (and separately transcript _IDs) after a Hisat2 ->samtools sort -> stringtie -> DEprep.py workflow.
DEprep.py outputs a ...
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Is it possible to integrate multiple gene expression datasets and use it for WGCNA?
I have 8 RNA-seq datasets and am interested in looking at genes co-expressed with a specific gene.
Among 8 RNA-seq datasets, 6 have less than 20 samples. Rather than working on each dataset ...
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select highly variable genes out of dataframe
lets say I have the following dataframe:
...
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WCGNA - Relate modules with Y features when the % of variance explained of each eigengen is low
I'm doing a WCGNA analysis (signed network) on microbiome 16S data.
I have transformed counts to centeres log-ratio transformed data (CLR) to address the compositional characteristics of the data and ...
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Avoiding false anticorrelations between individual genes per cell in single-cell RNAseq
When analysing a single-cell RNAseq dataset, one question I like to ask is: At a single-cell level, are these two genes correlated (expressed together) or anticorrelated (only one or the other is ...
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What codes represent what genes?
I want to run experiments on the data used in PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF link
So far, the paper has reduced the dimension to
ammon's ...
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Is loss/gain of function reflected in RNA-seq transcript counts?
Do LoF/GoF transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification?
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How should I interpret DGE results if only one HLA-A gene shows up as significant but not the others?
I have done a DGE recently and have been looking at the DGE list. One of the genes is HLA-A. However, when I dug deeper I realised there are hundreds of HLA-A genes with unique ENSEMBL number (of ...
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Expression analysis of miRNAs with normal RNA-seq data without small RNA-seq data
I am looking to perform expression analysis of miRNAs with normal RNA-seq data lacking small RNA-seq data?
Which path should I choose for known miRNAs and unknown new miRNAs?
Data set: rna-seq data ...
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Genome-guided transcriptome reconstruction: should I filter my reference annotation by transcript_support_level or other tags?
Is there really any advantage to filtering the GTF annotation for transcriptome reconstruction (or, for example, for pseudo-alignment quantification)? Are there any downsides (i.e. reasons why I ...
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GSEA. Subsetting Gene Ontology, Biological Processes, by gene set families of interest
I have run GSEA - on Gene Ontology , Biological Processes (GO and BP hereafter) - on some Mouse bulk RNA-seq data, and am currently in the process of going through the results. To do this, I have used ...
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Can multiplexing in Sequel II SMRTcells reduce the coverage?
I would like to have high depth of coverage of the transcriptome, but I need to analyze several tissues. I was suggested to pool all 5 tissue samples in same SMRT 8M cell. Will this result in a ...
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How can Iso-Seq reverse transcriptase artifacts be avoided?
My end goal is annotate a de-novo assembled genome. When trying to select the best method for transcriptome assembly I read Iso-seq was the preferred method. However other people suggested Nanopore as ...
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Transcriptome analysis
I am trying to assemble reads belonging to two different readlength. Is it a valid way since I am looking for common genes among the species I am assembling.
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RNASeq NMF clustering using what kind of expression unit?
I would need some help regarding certain points in a RNASeq gene expression analysis (sorry if there are stupid questions, its my first project and i have no capable supervision). My workflow is the ...
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Tool for cross referencing a newly found MOTIF to database of known MOTIFS
I need a tool or a function I can use in my code (R, or Python) that I can cross reference a MOTIF against known MOTIFS, a function that will take as input a MOTIF (a probability weight matrix, PWM ...
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How to use the contrast function in ebayes for making different comparisons
The design matrix i have is this I would like to know how to use they way its done in deseq2 where we can use the contrast function to make particular comparison
The code im running to make ...
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How to assess quality of WGCNA module identification in blockwisemodules()
I'm exploring WGCNA for bulkRNA sequencing analysis with human subjects. I have healthy, myocarditis, and heart failure patients (which can be further broken into ischemic or nonischemic)
I have been ...
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Gene/protein expression specific to a group in omics
I am wondering what is the significance of finding a particular protein specific to a disease or control group? when we detect 1000s of proteins in a proteomics experiment, how can one be sure that ...
