Create transcript region track (analysis)

Analysis title

Create transcript region track

Provider

geneXplain GmbH

Class

UTRTrackCreator

Plugin

com.genexplain.analyses (geneXplain analyses)

Description

This tool creates a sequence track with the selected UTR regions (5' or 3'), 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' end, e.g. 1st exon or 2nd intron, or alternatively from the 3' end by negative position numbers.

If some annotation does not exist, e.g. a transcript does not contain a 3rd exon or a 3'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