User:Nbertin/CAGEscan driven annotation protocol: Difference between revisions
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[[Category:Methods_and_Protocols]] |
[[Category:Methods_and_Protocols]] |
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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> |
[[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<br> == |
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Revision as of 10:56, 31 March 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
