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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4
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1answer
724 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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1answer
553 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),...
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0answers
101 views

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 ...
5
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2answers
871 views

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 ...
4
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3answers
879 views

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 (...
5
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2answers
180 views

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) ...
7
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1answer
953 views

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: $$C = L*N / G$$...
8
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0answers
120 views

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 ...
5
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1answer
146 views

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. ...
6
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3answers
440 views

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 ...
6
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1answer
329 views

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 ...
4
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3answers
699 views

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.) ...
18
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4answers
7k views

How to compute RPKM in R?

I have the following data of fragment counts for each gene in 16 samples: ...
10
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1answer
217 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 ...
14
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2answers
3k views

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 ...
15
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2answers
2k views

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 ...
5
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2answers
13k views

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 ...

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