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

I have 25 highly differentially expressed genes among responder (TRG12) and non responder (TRG45) patients to chemotherapy. I have made a neural network of these genes. Accuracy of model is 0.73 but ...
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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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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 simulate 3' end tag-based single-cell RNA-seq reads? For example, Drop-seq, 10X Chromium, CEL-seq, etc.. I see there are tools that simulate scRNA-seq gene count data (e.g. ...
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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

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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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 to assemble transcriptomes from a species without a reference genome using a combination of Iso-seq and illumina data. One example I saw (Li et al 2017), used the ...
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Merge / Reconciliate several de novo transcriptome assemblies with different kmers

I am trying to build a De Novo transcriptome reference assembly for an eukaryotic organism. I've created several assemblies with rnaSpades using different kmer sizes (19 to 69 with step 10). Now I ...
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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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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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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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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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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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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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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),...
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How do I compare transcriptomes of the same species across different developmental stages?

I want to identify the most highly expressed genes across several developmental stages of a given insect, in hopes of identifying a protein that can be used to design an insecticide. I have a few ...
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Difference between de novo transcriptome assembly methods

I have been looking around (including read the original papers) to understand what is essentially the difference between StringTie in non-reference based mode (de novo) and Trinity de novo assembly. I ...
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How to compare transcriptomic profiles of two cell types (single cell RNA-seq)?

I found this interesting Single RNA-seq data set in GEO, but I am not sure how to analyze it appropriately. They have deposited transcriptomic profiles of human and mouse pancreatic islets (...
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RapMap: reference transcriptome for simulated reads

I am very new to bioinformatics and trying to repeat the benchmark in the RapMap paper with an experimental tool working in a similar but different fashion. In the paper (taken from their github) ...
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Coverage calculation: long reads (RNA-seq)

Say your aim is to calculate the coverage of an RNA-seq experiment generated with long-read sequencing (so, uneven read length). Up to now, I relied on the Lander/Waterman equation: $$C = L*N / G$$...
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Run cuffcompare in strand-agnostic mode

Is there a way to run Cufflinks' cuffcompare in a strand-agnostic mode? I would like to do this because I have some RNA-seq datasets derived from an unstranded run, that should be compared to a ...
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Documentation for Transfrag class codes (cuffcompare)

Is there any extensive documentation or description for each class of Transfrag class codes as reported by the cuffcompare tool in the Cufflinks package? Official doc might not be the best. E.g. ...
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tools to reconcile experimental transcripts with reference annotation

Looking for tools to reconcile alignment file of experimental transcripts mapped to genome (SAM/BAM) with the reference transcriptome annotation (GTF) from Ensembl (organism: D. melanogaster). The ...
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PASA pipeline: compare experimental transcripts to the reference annotation

I would like to ask if anyone has experience in running a subset of the PASA pipeline, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation. In more ...
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Analysis of differential transcript usage (DTU)

Recent breakthroughs in bioinformatics tools for quantification (e.g. Cufflinks/Kallisto/Salmon etc.) and tools which can identify differential transcript usage (DTU) (e.g. DRIMSeq, Cufflinks etc.) ...
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How to compute RPKM in R?

I have the following data of fragment counts for each gene in 16 samples: ...
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182 views

Linear models of complex diseases

A popular framework to analyze differences between groups, either experiments or diseases, in transcriptomics is using linear models (limma is a popular choice). For instance we have a disease D ...
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Normalization methods with RNA-Seq ERCC spike in?

ERCC spike-in is a set of synthetic controls developed for RNA-Seq. I'm interested in using it to normalize my RNA-Seq samples. In particular, I'd like to use the spike-ins to remove technical bias ...
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Alignment based vs reference-free (transcriptome analysis)?

I want to focus on transcriptome analysis. We know it's possible to analyze RNA-Seq experiment based on alignment or k-mers. Possible alignment workflow: Align sequence reads with TopHat2 Quantify ...
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What is the difference between a transcriptome and a genome? [closed]

I have a computer engineering background, not biology. I started working on a bioinformatics project recently, which involves de-novo assembly. I came to know the terms ...