Question about the 'get flanks' tool

Hi all,

I’m using Galaxy to get terminator regions for all genes in a genome and I’m using the ‘get flanks’ tool.

Question: does get flanks define the 3’ end of the gene on the sense strand as the ‘Around end’ regardless of the direction of transcription? So if the gene is transcribed from the antisense strand, get flanks would be taking the flanking region around the transcription start site…?

I hope this makes sense, but let me know otherwise.



Cross-posted on biostars: Question about the 'get flanks' tool in Galaxy

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Thanks Ram


If you include the strand in the BED6 input, the tool will extract upstream/downstream correctly. For any BED dataset (Genome Browser FAQ), the coordinate numbers are always with respect to the forward strand but which bases those represent depend on the strand assignment.

Scroll down on the tool form for the examples: both are extracting the same coordinates on different strands as output. Those are based on different stranded inputs combined with some same parameters and some different parameters set on the form.

If you are not sure or want to check settings against your data: try running the tool on a small sample that includes both strands and visualize the results in IGV.

Thanks @RamRS for linking to two posts together :slight_smile:

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Thanks @jennaj , this makes sense!