Difference between revisions of "XENLA Oktoberfest"

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(Created page with "This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset. = Input data == * JGIv6 scaffold * Reference cDN...")
 
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This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset.
 
This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset.
  
= Input data ==
+
= Input data =
 
* JGIv6 scaffold
 
* JGIv6 scaffold
  
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= Analysis procedures =
 
= Analysis procedures =
 +
 +
= Known issues =
 +
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-3 sequences per genomic region), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release.
 +
* Some genomic regions do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release.
 +
 +
= Plan =
 +
* Next release is planned near Thanksgiving, 2012.
  
 
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[[Category:Xenopus_Genome_Project]]
 
[[Category:Xenopus_Genome_Project]]

Revision as of 10:36, 18 October 2012

This is a page for integrated gene models of Xenopus laevis, released in October, 2012. "Oktoberfest" is a name of dataset.

Contents

Input data

  • JGIv6 scaffold
  • Reference cDNA/EST
    • From XenBase
    • Mike Gilchrist's EST collection (mgEST*)
    • John Quakenbush's EST collection (TC*)
    • JGI's cDNA collection (XeXen*)
  • Assembled transcripts

Analysis procedures

Known issues

  • Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-3 sequences per genomic region), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release.
  • Some genomic regions do not have tree figures, because of newick utilities error. It will be fixed in next release.

Plan

  • Next release is planned near Thanksgiving, 2012.