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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27 views

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 kalisto for sequence alignment in Galaxy. i found this field empty: there is no option available for the reference transcriptome. how I can get one? Can I let the other configuration by ...
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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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37 views

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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145 views

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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49 views

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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68 views

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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normalizing transcript-level expression data

Generally, RNA-seq analysis tools like edgeR or DESeq2 work on gene-level data. For differential expression (or differential transcript usage), transcript-level data has its own caveats. However, for ...
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GTF parser returned Empty DataFrame

I used the following script to retrieve for RPKM and cov value for each transcript. ...
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Which of the Transcriptome assembly method is best for identifying novel lncRNAs?

I'm working with human samples and I'm trying to identify novel lncRNAs from tumor samples of Prostate cancer. I'm using reference based transcriptome assembly with ...
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48 views

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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179 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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119 views

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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41 views

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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78 views

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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54 views

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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370 views

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 ...
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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. ...
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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 ...
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2k views

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 ...
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107 views

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 ...
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703 views

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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How to highlight specific cells in Seurat 2.4

I used Seurat 2.4 on our scRNA dataset to obtain the following tSNE plot.I was able to successfully extract cell IDs from the different clusters, and generate gene expression profiles. The analysis, ...
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Transcription factor targets for Human and Mouse genes

I want to get transcription factor targets for my list of genes (For Human and Mouse) I have found ENCODE Transcription Factor Targets database (The link is given below). But I am looking for some ...
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Merging transcriptomes coming from different experiments

I'm planning to build a transcriptome by pooling all existing transcriptomes in SRA for a non-model species (which has no reference genome) to study differentially expressed genes and the like. It ...
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419 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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72 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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93 views

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

I have 25 highly differentially expressed genes among and patients to chemotherapy. I have made a neural network of these genes. The accuracy of the model is 0.73 ...
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113 views

scRNA-seq differential transcript usage

Many of the modern gene-quantification tools (Salmon/Kallisto) output transcript-level (as opposed to gene-level) data. All of the scRNA-seq analysis I have seen just uses the gene-level values. I ...
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29 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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Simulating 3' end tag-based scRNA-seq reads

Are there any tools that will simulate 3' end tag-based single-cell RNA-seq reads? For example, Drop-seq, 10X Chromium, ...
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Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix

I have a list binding site motif of SP1 transcription factor which collects from PWMScan tools. Actually this tool scan whole human genome and give the entire binding motif list. From that list of ...
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At what stage of a transcriptome assembly is it better to perform read contaminant filter?

I'm trying to assemble a bivalve transcriptome. Since bivalves are filter feeders, their transcriptomes tend to be highly contaminated by bacteria, algae and whatnot. Since I pooled several ...
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RNA-Seq type and and optimal fusion detection [closed]

There are several popular types of RNA-Seq library prep which are frequently used: total RNA (with and without ribosomal depletion), mRNA-Seq/poly-A, and targeted mRNA-Seq/RNA exome. What would the ...
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361 views

Reproducing GTEx transcriptome analysis

I am willing to reproduce part of the analysis from "The human transcriptome across tissues and individuals" (Melé et all, 2015). I downloaded GTEx v6 FPKM data in txt format from GTEx portal. I want ...
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What is the current state-of-the-art in assembling hybrid transcriptomes?

We are considering attempting de novo assembly of a species transcriptomes (i.e. without a reference genome) using the combined NGS outputs of Iso-seq and Illumina. One example I saw (Li et al 2017),...
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116 views

Merge / Reconciliate several de novo transcriptome assemblies with different kmers

I am building a De Novo transcriptome reference assembly for an eukaryotic organism for which I have a genome. I've created several assemblies with rnaSpades using different kmer sizes (19 to 69 with ...
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gene-level versus transcript-level analysis

Traditionally, RNA-seq data was quantified on gene level. Newer methods quantify on transcript/isoform level. For example, Kallisto only outputs transcript-level abundances. From the DESeq2 vignette: ...
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Variability in genes across platforms

I have a matrix of gene expression for single cell (cells in column and genes in row) in 9 time points with about to 200 cells for each time point. I have also a matrix of gene expression in bulk RNA-...
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Batch detection of CRISP proteins in fasta file

Probably a naive question. I am inexperienced. I am interested in identifying potential CRISP (Cysteine-rich secretory proteins) in a certain tissue transcriptome (ca. 20k sequences in fasta). I ...
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273 views

Reduce number of transcripts in a highly variable de novo transcriptome assembly

I have a de novo assembly using both multiple SRA and locally sequenced transcriptomes. I started with 270M PE reads from 9 tissues. Here are the assembly stats generated with ...
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96 views

Correct way to assemble reference transcriptome - what's --samples_file option in Trinity?

I have 101 samples from 9 tissues of a nonmodel species, coming either from SRA or sequenced by my lab. I want to generate a reference transcriptome with Trinity for further analysis. In order to do ...
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191 views

What is “Possible polymerase run-on fragment”?

I used gffcompare recently to compare a newly assembled transcriptome and a published transcriptome. The class code "p" transcripts are "possible polymerase run on". What does that mean? I tried very ...
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712 views

What process and input data is required for a cellranger reference transcriptome?

I'm analysing single-cell RNA-Seq data using the 10X Genomics cellranger platform. While they provide reference data for Mouse and Humans, other species require a ...
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628 views

Hierarchical models with limma?

I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
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497 views

Command not found error on HISAT2

I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. I am able to successfully generate an index (using the hisat2-build command),...