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Question: A question of concept?
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gravatar for syrez.m
3.0 years ago by
syrez.m • 0
syrez.m • 0 wrote:

Hi all!

I'm new to this so, pardon my noobness.

If I were to convert the transcript annotations from a GTF into BED format, how many BED records would be generated? Would it be equal to total number of transcripts in the GTF file? One BED record for each transcript?

 

Thanks!
bed gtf records • 736 views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by syrez.m • 0
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool Convert Formats > GFF-to-BED converter will create one BED line per line in the original GFF/GFT dataset. The result is a BED6 dataset (the first 6 columns of full BED format). These are commonly interpreted to be individual "exons" but that is not necessarily the case - the actual BED content depends on the original GFF/GTF input content.

If instead you wish to have a BED12 result (combining regions/exons into a single record - often used to represent a transcript), then there are command-line tools from UCSC available in their Downloads area under Source. For MAC OSX, the location would be here.

Many of these UCSC utilities have been wrapped for Galaxy and are available in the Tool Shed (for use in a local or cloud Galaxy), but I do not believe that the ones needed to produce a BED12 have been yet (gtfToGenePred & genePredToBed). I could be corrected here though!

BED format specification

Hopefully this helps, Jen, Galaxy

 
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jennifer!

ADD REPLY • link written 3.0 years ago by syrez.m • 0
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