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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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 ...
user18959's user avatar
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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 ...
shaimaa Hassan's user avatar
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overrepresentation test, between transcriptome and candidates sequences obtained from the transcriptome

For an analysis of my data, I have a transcriptome and a list of sequences obtained from the transcriptome. I would like to perform a functional enrichment analysis. I have annotated both sets of data ...
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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 ...
Hirak Sarkar's user avatar
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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 ...
Sudoh's user avatar
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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 ...
Adi's user avatar
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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 ...
David's user avatar
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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 ...
Avamys's user avatar
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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 ...
MrPapouille's user avatar
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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 ...
Emily Nwo's user avatar
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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 ...
Shakunthala's user avatar
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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 (...
Angus Campbell's user avatar
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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. ...
Tom's user avatar
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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. ...
Abhishek Pandey's user avatar
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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 ...
Tangent Runner's user avatar
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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 ...
Smiletree's user avatar
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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 ...
pietro_molina's user avatar
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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,...
phytofan's user avatar
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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 ...
Kishor Kumar Sarker's user avatar
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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 ...
Christa Frodella's user avatar
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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 "...
pietro_molina's user avatar
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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 ...
CephBirk's user avatar
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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 ...
gringer's user avatar
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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 ...
Sashko Lykhenko's user avatar
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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 &...
gc5's user avatar
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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-...
Manuel Sánchez Mendoza's user avatar
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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 ...
the_darkside's user avatar
3 votes
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335 views

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 ...
Dunois's user avatar
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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 ...
Anthony Guterres's user avatar
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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 ...
RoB's user avatar
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REMC SNP annotations for transcriptome prediction - epiXcan

I have been trying to use a pipeline for predicting gene expression for a target gene (Although you can do it for many) - the name of this method is epiXcan. Here is a link to the paper: https://www....
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Importance of Proper Pairs vs Aligned Reads for RNASeq data

I have stranded, paired end RNASeq reads that I have aligned using STAR. I plan do conduct a differential expression analysis with DESeq2. After running quality control checks, a good portion of my ...
Tomas Bencomo's user avatar
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What are the meanings of these transcript ids?

I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser. ...
MudithMMBc's user avatar
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How to analyze expression of certain group of genes in certain types of cell?

I need to analyze expression of ~ 400 genes with a certain function in the embryonic stem cells. All these genes are combined into one database with RefSeq IDs. What is a recommended workflow to ...
Ina Izumi's user avatar
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How to visualise /add Arabidopsis T-DNA Lines As Tracks On IGV

We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines by loading them on IGV. As a control we ...
Dendrobium's user avatar
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How to find novel transcripts using GFFcompare?

I am trying to find novel transcripts from an RNA-seq database. Based on the advice I got, it seemed that using Stringtie for transcript assembly is a good way to go, and it supports novel transcript ...
user1995's user avatar
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Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
iamakhilverma's user avatar
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What are the right parameters to trim a small RNA transcriptome with trimmomatic?

I'm having some problems with finding the right parameters to trim my small RNA Illumina reads (51 nt long) with Trimmomatic. Before trimming, one of the samples (21M reads) looks like this: So for ...
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