Difference between revisions of "XENLA Oktoberfest"
From Marcotte Lab
(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...") |
|||
Line 1: | Line 1: | ||
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 | ||
Line 13: | Line 13: | ||
= 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. | ||
---- | ---- | ||
[[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.