Difference between revisions of "TXGP ens63 reference"

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== Introduction ==
+
= Introduction =
  
 
The goals of TXGP RNA-seq analysis is (1)to construct gene models in ''X. laevis'', and (2) estimate their expression levels in different tissues. However, many de novo transcriptome assembly program generates 'false positive' transcript models. Also, because we do not have a genome sequence yet, it is hard to derive gene models from transcripts directly (esp. in allotetraploidy condition). So we are using [[http://www.ensembl.org EnsEMBL]] annotation as a reference of gene model construction.
 
The goals of TXGP RNA-seq analysis is (1)to construct gene models in ''X. laevis'', and (2) estimate their expression levels in different tissues. However, many de novo transcriptome assembly program generates 'false positive' transcript models. Also, because we do not have a genome sequence yet, it is hard to derive gene models from transcripts directly (esp. in allotetraploidy condition). So we are using [[http://www.ensembl.org EnsEMBL]] annotation as a reference of gene model construction.
  
== Genes & Transcripts ==
+
= Genes & Transcripts =
 
http://www.marcottelab.org/users/XenopusData/ens63/ens63_gene_tx.png
 
http://www.marcottelab.org/users/XenopusData/ens63/ens63_gene_tx.png
  
 +
= Clustering of transcripts to gene
 
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[[Category:XenopusGenome]]
 
[[Category:XenopusGenome]]

Revision as of 12:39, 12 October 2011

Introduction

The goals of TXGP RNA-seq analysis is (1)to construct gene models in X. laevis, and (2) estimate their expression levels in different tissues. However, many de novo transcriptome assembly program generates 'false positive' transcript models. Also, because we do not have a genome sequence yet, it is hard to derive gene models from transcripts directly (esp. in allotetraploidy condition). So we are using [EnsEMBL] annotation as a reference of gene model construction.

Genes & Transcripts

ens63_gene_tx.png

= Clustering of transcripts to gene