User:Nbertin/CAGEscan driven annotation protocol: Difference between revisions

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(CAGEscan driven annotation protocol)
 
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[[Category:CAGEscan]]
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&nbsp;&nbsp; CAGEscan paired-end data link TSS to a downstream sequence. By annotating those downstream sequence with respect to know transcript feature (exon, intron, UTRs) it is possible to extend the annotations of (HelicosCAGE derived) TSS by comparing them to CAGEscan derived TSS. This can be accomplished either by comparing data arising from similar biological samples or comparing it to the full body of CAGEscan-derived TSS annotation files<br>
[[Category:Methods_and_Protocols]]


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&nbsp;&nbsp; [[CAGEscan]] paired-end data link TSSes to downstream sequences. By annotating those downstream sequence with respect to know transcript(s) and transcript feature(s) (exons, introns, UTRs) it is possible to extend the annotations of (HelicosCAGE derived) TSS or TC by comparing them to such annotated CAGEscan derived TSS. Note that his can be accomplished either by comparing data arising from similar biological samples or comparing it to the full body of CAGEscan-derived TSS annotation files<br>
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== CAGEscan-derived TSS annotation<br> ==


=== CAGEscan-derived TSS annotation file construction<br> ===
== CAGEscan-derived TSS annotation<br> ==


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=== CAGEscan-derived TSS annotation file construction<br> ===
*&lt;edit&gt;

*sample file<br>
*script


=== CAGEscan-derived TSS annotation files<br> ===
=== CAGEscan-derived TSS annotation files<br> ===


*&lt;edit&gt;
*&lt;edit&gt;


=== Combining CAGEscan-derived TSS annotation files and (Helicos)CAGE clusters<br> ===
=== Combining CAGEscan-derived TSS annotation files and (Helicos)CAGE clusters<br> ===


*Input
*Input


BED/OSCfile CAGE cluster<br>
BED/[http://fantom.gsc.riken.jp/4/download/Tables/doc/090703-osctable.rtf OSCfile] CAGE cluster<br> BED CAGEscan annotation file
BED CAGEscan annotation file


*Output
*Output


Annotated CAGE cluster OSCfile
Annotated CAGE cluster OSCfile


<br>
<br>

Latest revision as of 15:19, 7 September 2011


   CAGEscan paired-end data link TSSes to downstream sequences. By annotating those downstream sequence with respect to know transcript(s) and transcript feature(s) (exons, introns, UTRs) it is possible to extend the annotations of (HelicosCAGE derived) TSS or TC by comparing them to such annotated CAGEscan derived TSS. Note that his can be accomplished either by comparing data arising from similar biological samples or comparing it to the full body of CAGEscan-derived TSS annotation files

CAGEscan-derived TSS annotation

CAGEscan-derived TSS annotation file construction

  • sample file
  • script

CAGEscan-derived TSS annotation files

  • <edit>

Combining CAGEscan-derived TSS annotation files and (Helicos)CAGE clusters

  • Input

BED/OSCfile CAGE cluster
BED CAGEscan annotation file

  • Output

Annotated CAGE cluster OSCfile


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