Question about the 'get flanks' tool in Galaxy

Question

[David]

Hi all,

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

Get flanks defines 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.

Thanks,

David

[Ram]

Please search/ask: https://help.galaxyproject.org/

[GenoMax]

A tool should work logically irrespective of the strand it is working on so it would be surprising if it did that. Region before TSS would also be at 5'-end on that strand.

But do ask on galaxy support site as @Ram said.

[David]

This is what I thought, but I've checked manually with the extracted coordinates in UCSC genome browser and it's taking the end site as the sense strand 3' gene region regardless of the direction of transcription. I've not seen this mentioned anywhere, it's puzzling...

Yes thanks both, I've now posted this on the galaxy support site.

[GenoMax]

Ah so it is doing something even more unusual, if it is retrieving data from 3'-end of sense strand.

[Ram]

When you cross-post (something you should avoid), at least link to other posts so people can look at all relevant information in an easier way. Link to post on galaxy help: https://help.galaxyproject.org/t/question-about-the-get-flanks-tool/8533

[David]

Oh apologies, will do! Sorry, I'm new to this.

Answer 1

[David]

This was resolved in https://help.galaxyproject.org/t/question-about-the-get-flanks-tool/8533