Questions tagged [transcriptome]
The set of all transcripts of a biological entity, e.g. the transcriptome of a single cell, of a tissue, of an organ, of an individual, of a species. Can also be used to refer to a subset of the transcriptome, e.g. the polyadenylated transcriptome, given that often experiments ignore the 99% of transcripts that are ribosomal RNAs.
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How to only enrich sensible GO and KEGG terms?
I'm thinking of analyzing enriched pathways using KEGG and GO databases on de-novo assembled transcripts using clusterProfiler 4.0. After annotating them with ...
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Should I include unannotated transcripts in a pathway enrichment analysis of a de-novo assembled transcriptome?
I'm trying to perform an enrichment analysis on a set of Transcripts assembled de-novo, using a GSEA like method on KEGG and GO. The set contains annotated and unannotated transcripts. My question is:
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Why is RNASpades giving three FASTA output files instead of only one?
I'm running RNASpades for de-novo transcriptome assembly in the Galaxy workflow manager
. Instead of giving only one output of ...
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I have assembled raw short RNA-seq reads into Transcripts using Trinity. My raw reads were strand-specific. What should I set "--strand" in Diamond?
I used Trinity to de-novo assemble my RNA seq raw reads. These reads were generated using a strand-specific method. Now I want to do a BLASTx using Diamond. I am unsure what I should keep under its ...
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How to identify a bacterium species from its short RNA-seq transcriptomics data?
I am new to RNA-seq analysis and wanted to ask if there is a method to reliably identify the species of a microbial organism using only its raw short RNA transcriptomics data. Here are some of the ...
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Figuring out operons from prokaryotic RNA-Seq data
I am looking at a couple of unpaired prokaryotic RNA-Seq datasets. These data have been obtained from bacteria (cultures likely axenic, not guaranteed). My aim is to figure out whether my genes of ...
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Assessing the quality of an assembly
I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda....
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Most-abundant isoform identification using 10x scRNASeq 5' short-reads
I have read a couple of publications related to the question being asked here, and have concluded that quantification of isoforms for scRNASeq experiments is typically coupled with long-read ...
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Is it possible to integrate a bulk and a pseudobulk (previously scRNA or snRNA seq) dataset
I have recently sequenced a bulk dataset. However one of my conditions has a lot of contamination from other cell types. I was thus thinking of using a publicly available single-cell dataset of my ...
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After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?
I have been running nf-core in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA ...
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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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Low fraction reads in cell metric in snRNA-seq data
For some of our snRNA-seq samples we are finding low fraction of reads detected in single-nuclei rna-seq samples from cellranger, while the other metrics are perfect.
While I understand this could be ...
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Transcript vs Primary transcript on phytozome
Could someone help me understand what the difference between transcript and primary transcript on phytozme is? For example, this dataset of A.thaliana has "primary transcript CDS" vs CDS.
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pyScenic CLI for ctx is giving error: Not a single module loaded
Hi I ran pyScenic's ctx via the command in command prompt:
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How to find specific types of assemblies for specific species using entrez tools?
How to find specific types of assemblies for specific species using entrez tools?
Task: Trying to specifically find transcriptomes and associated cDNA data for a list of speices.
I can use this ...
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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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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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MAGs transcriptomics pipeline question
I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
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How can to validate the presence of a certain type of cells in a single cell dataset?
I have a single cell dataset which I consider to be a reference , let say, for an human organ, I have identified some new clusters that correspond to cell types. I also have WGCNA modules that ...
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Are the doublets in the tutorial dataset in Scanpy/ Seurat already filtered?
I noticed the tutorials that Scanpy and Seurat use do not demonstrate doublet removal in their down stream analysis.
Is the dataset output of cellranger count already doublet removed or do I need to ...
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Trinity de novo transcriptome assembly: samtools view failed to add PG line to the header
I have assembled the transcriptome a plant species using Trinity.
Here is the command:
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System specifications for NGS data analysis
I have a 3.7 GB whole genome data of a eukaryote, for which genome assembly, gene prediction, and annotation steps have to be performed. In some time I would also need to analyze the transcriptome ...
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Normalization methods to combine scRNA-seq experiments with different sequencing depths
I am training a classifier to identify a cell type in a particular state of activity using scRNA-seq. There is a large variation in the sequencing depth (reads average per cell) of the testing data (...
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RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias
I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters.
Aim We would like to conduct SNP discovery of these samples.
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How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?
I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. ...
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Why is bulk RNA sequencing reflecting AVERAGE expression but not TOTAL expression of all cells?
When I am reading papers that compares bulk RNA sequencing and single-cell RNA sequencing, we often see papers describe bulk RNA seq measures the average cell expression.
For example, in this paper ...
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Pros and cons between genomes and transcriptomes?
What are the major differences between the use cases of a shot-gun genome and an mRNA capture transcriptome? Especially when it comes to downstream analyses such as looking for orthology, and ...
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Length of Contigs in Transcriptome and Whole Genome Assembly
Why are there shorter contigs from transcriptome assembly than from a whole genome assembly? I know the difference between transcriptome and genome, but don't really understand what contigs are in the ...
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How to find an unidentified splicing variant of a protein?
I have some data indicating there might be a splicing variant of the Arabidopsis Thaliana protein I'm studying that has not been identified. Is there a database of i.e. RNA sequences (transcriptome?) ...
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how can I get expression of an inserted foreign genes?
hi we have transgenic mice with human gene inserted. if we profom rnaseq for the mice, how can we get the expression value of the human gene inserted to the mice? and use this expression to compare ...
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How to simulate replicates for DGE analysis?
I am prototyping with data visualization of DGE results, and I would like to work on the analysis pipeline before the real data is available. Currently, I only have 3 samples for wild type and 1 ...
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Alternatives to CAP-miRSeq for microRNA processing
I am involved in a Drosophila transcriptomics project in which we have RNAseq data for small RNAs (for microRNAs) in addition to total RNA (for mRNAs).
The total RNA reads have been analysed ...
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Transcriptomics vs Proteomics for understanding molecular responses [closed]
I am planning some experiments to investigate how mono cultures of microbes respond to different nutrient concentrations. I want to use an -omics based approach to understand how, on a molecular level,...
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Hisat2 compatibility for long reads (Pacbio)
I am working with a high performance cluster computer containing 112 threads. I am trying to align PacBio transcriptome reads against the genome to count the gene number. For pair end read i used the ...
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Splice variant analysis with ensembl genome/annotation/rna. Which files do I use?
I am running splice variant analysis. I wanted to use NCBI genome but the program works better with ensembl. I am a bit confused on primary vs. top level to use as my reference genome. I also do not ...
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How to download data from SRA in Linux systems via the command line?
My workflow for downloading data from SRA has been the following:
Access SRA Run Selector.
Enter the accession number for the project of interest.
Download "Accession List" for the "...
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Trinity assembly from many samples
When you combine samples for de-novo transcriptome assembly with Trinity, do you suggest limiting the number of reads for each sample? I had read one of Matthew MacManes' papers awhile back suggesting ...
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use Kallisto in galaxy
I want to use Kallisto for sequence alignment in Galaxy. Its description is:
a program for quantifying abundances of transcripts from bulk and
single-cell RNA-Seq data, or more generally of target ...
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How do I increase the sensitivity of Salmon Alevin?
I'm in a little bit of a bind with targeted single-cell sequencing. I'm trying to match up our reads to the targeted amplicon panel (418 targets), and all but one have matched successfully with Salmon ...
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RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation
I have some transcriptomic (Whole) sequencing data that I should analyse. I would like to do raw data alignment to a reference genome taking into account the multi mapped reads and uniquely mapped ...
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Calculating most abundant transcript from RNA-Seq data
vcf2maf uses VEP to annotate variants, and I believe selects the default Ensembl transcript to use for annotation. Sometimes the ...
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How to check if a given gene is expressed in a group of microarray samples if I do not have control group to compare with?
I have a microarray gene expression dataset consisting of placenta samples. I want to check whether these placenta samples are mixed with maternal decidua tissue. I have marker genes for decidua ...
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Required input files for StringTie2
I am working on a virtual project for WGS combined with RNA seq for annotation. The RNA will be sequenced using PacBio Isoseq (Sequel II, HiFi-reads). With some research, I found that StringTie2 is ...
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Genes associated with digestion in single cell RNASeq
I am reading Saunders et al. (2018).
In the methods' subsection "ICA based analysis and clustering" (independent component analysis), a set of independent components from ICA is labelled as &...
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PacBio long-reads impact in transcriptome de novo assembly?
We are strongly interested in assembly a good transcriptome of reference for a non-model organism and build a local database. We have sequenced the same individual with Illumina (150 millions of pair-...
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Basic question about finding mRNA sequence in transcriptome
I am a computer scientist just starting out in bioinformatics topics, and would appreciate any guidance that can be given here:
I have an mRNA sequence- an isoform - whose length is about 4000 base ...
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Difference between isoforms and paralogs in transcriptoms?
I've assembled RNAseq data into a transcriptoms using Trinity. There's a option to keep only the longest isoforms for each transcripts and it lead me to wonder how it deals with duplicated genes (--&...
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Decontaminating RNA seqs for de novo transcriptome assembly and annotation of novel eukaryotes
I have raw paired-end RNA-seq reads for two novel eukaryotic species. Some background: the reads represent a copepod (arthropod) species each. The mRNA for each read set was obtained by extracting ...
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How to understand and analyse RNA-seq data (for a beginner)?
I am trying to understand expression of a certain protein across Pseudomonas species. I downloaded an SRA file from NCBI and converted it to a fastaq file. I am not able to understand how to interpret ...
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What RNA-Seq expression value would be closest to Microarray equivalent?
I know this question may seem strange.
I'm using Spearman correlation between gene expression profiles for various reasons (I won't go into details here). As a result, I often compare RNA-Seq and ...
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