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Protected "Create transcript region track (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

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2020-12-09T11:14:46Z

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;Analysis title
:[[File:Data-Create-transcript-region-track-icon.png]] Create transcript region track
;Provider
:[[geneXplain GmbH]]
;Class
:{{Class|com.genexplain.analyses.UTRTrackCreator}}
;Plugin
:[[Com.genexplain.analyses (plugin)|com.genexplain.analyses (geneXplain analyses)]]

=== Create a track of UTR sequences for transcripts ===

=== Description ===

This tool creates a sequence track with the selected UTR regions (5<nowiki>'</nowiki> or 3<nowiki>'</nowiki>), promoters, exons or introns for the provided transcripts. Since UTRs can be long one can choose to use only a certain length of bases from the end as UTR. Exons or introns are specified by their position in the primary transcript from the 5<nowiki>'</nowiki> end, e.g. 1st exon or 2nd intron, or alternatively from the 3<nowiki>'</nowiki> end by negative position numbers.

If some annotation does not exist, e.g. a transcript does not contain a 3rd exon or a 3<nowiki>'</nowiki>UTR is not annotated, the transcript is not included in the output. For UTRs one can choose to substitute missing UTR information with the respective exon.

==== Parameters ====

* '''Input transcripts''' - Transcripts to extract UTRs for
* '''Species''' - Species of input transcripts
* '''Transcript region''' - Transcript region to extract
* '''First/last exon as UTR''' - Use first/last exon as UTR if otherwise not defined
* '''Fixed UTR length''' - Create UTRs of fixed length
* '''Ignore CDS information''' - Ignore CDS information and create fixed or exon length UTRs (Note that actual UTRs can be very long)
* '''Exon/Intron number''' - Exon/Intron number to extract (Specify 1, 2, ... for first, second, ... intron, or -1, -2, ... for last, second last, ... ex/intron)");
* '''Promoter start''' - First base of promoter relative to TSS
* '''Promoter end''' - Last base of promoter relative to TSS
* '''Output path''' - Path for output track or sequences

[[Category:Analyses]]
[[Category:Data (analyses group)]]
[[Category:GeneXplain analyses]]
[[Category:Autogenerated pages]]

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