Mapping transcriptome to genome

Malovaan

Junior Member

Join Date: May 2015

Posts: 2
Share

Post
#1

Mapping transcriptome to genome

07-08-2015, 07:17 AM

I'm wondering about the best way to determine the proportion of different transcriptome assemblies (assembled in trinity) which can be mapped to a reference genome assembly - basically for an indication of completeness.

I'm thinking that nucmer in the MUMer package might be a good place to start, with the transcripts as query and the genome as the reference sequence, but does anyone have a more cunning suggestion than that?

Thanks in advance!
Tags: None
yzzhang

Member

Join Date: Jan 2013

Posts: 67
Share

Post
#2

07-08-2015, 07:24 AM

the Sim4db http://www.ncbi.nlm.nih.gov/pubmed/21551146 and Exonerate https://www.ebi.ac.uk/~guy/exonerate/beginner.html work good

Last edited by GenoMax; 07-08-2015, 07:41 AM. Reason: fixed URL's
Comment

Previous template Next

Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool

by SEQadmin2

CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.¹ But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

Despite this, “CRISPR helped turn genome editing from a specialized technique into...
- Channel: Articles
Today, 11:01 AM
Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications

by SEQadmin2

Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

The systematic characterization of the human proteome has...
- Channel: Articles
07-20-2026, 11:48 AM
Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by SEQadmin2

Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...
- Channel: Articles
07-09-2026, 11:10 AM

Topics	Statistics	Last Post
New Genomic Method Uncovers Ancient Hominin DNA by SEQadmin2 Started by SEQadmin2, Today, 02:55 AM	0 responses 7 views 0 reactions	Last Post by SEQadmin2 Today, 02:55 AM
Study Captures the First Moments of DNA Replication by SEQadmin2 Started by SEQadmin2, 07-24-2026, 12:17 PM	0 responses 12 views 0 reactions	Last Post by SEQadmin2 07-24-2026, 12:17 PM
Chemotherapy Leaves Detectable DNA Signatures in Childhood Tumors by SEQadmin2 Started by SEQadmin2, 07-23-2026, 11:41 AM	0 responses 12 views 0 reactions	Last Post by SEQadmin2 07-23-2026, 11:41 AM
Single-Cell Atlases Skew Toward European Ancestry, Analysis Finds by SEQadmin2 Started by SEQadmin2, 07-20-2026, 11:10 AM	0 responses 24 views 0 reactions	Last Post by SEQadmin2 07-20-2026, 11:10 AM

Unconfigured Ad

Mapping transcriptome to genome

Comment

Latest Articles

ad_right_rmr

News