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Old 09-20-2010, 10:52 AM   #1
mmuratet
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Default GTF to BED converter?

Hello

cufflinks produces a gtf file of transcripts and I think it would be handy to be able to display this on the UCSC genome browser using the bigDataUrl method. Galaxy has a tool to go gtf -> gff3 and another gff3 -> bed from which one get get an indexed bigBed. Does anyone know of an existing tool that will take gtf -> bed?

Thanks

Mike
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Old 09-20-2010, 02:35 PM   #2
svl
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Quote:
Originally Posted by mmuratet View Post
Does anyone know of an existing tool that will take gtf -> bed?
Never used/tested it myself but the google search "gtf2bed" came up with: http://noble.gs.washington.edu/~shob...hs/bin/gtf2bed

If you know how to use a perl script you might want to try this.
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Old 09-20-2010, 05:17 PM   #3
mmuratet
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Thanks. It's always the simple searches. I'll give it a shot.
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Old 04-15-2011, 06:44 AM   #4
poisson200
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Default Displaying a custom track of transcripts from cufflinks

Dear Bioinformaticians,
Please can you tell me how to display a full genomes/transcriptomes worth of transcripts in the hg19 UCSC genome browser?

I make the assumption that a full transcriptome GTF file is too big to simply upload and I was thinking of writing a GTF to Bed script (then to bigbed) so I can display it.

The script linked here looks fine but it is a bit too simplistic and does not connect up exons. I can write my own but happy to use some other solution if it already exists.

Thank you in advance of any advice,

Kind regards,

John.
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Old 04-15-2011, 07:12 AM   #5
mmuratet
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Default Loading GTF files to the UCSC browser

You could use awk or perl or an equivalent to break the GTF file into pieces by chromosome. I've never tried it myself but it seems possible.
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Old 04-15-2011, 07:20 AM   #6
biznatch
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Quote:
Originally Posted by poisson200 View Post
I make the assumption that a full transcriptome GTF file is too big to simply upload and I was thinking of writing a GTF to Bed script (then to bigbed) so I can display it.
I have no idea how big the file is, but you can load files up to 500 MB and 100 million lines (sometimes more than 100 million) so maybe you don't have to break it up. Compress the file as a .gz for faster uploading (although in my experience the uncompressed file has to be smaller than 500 MB).

Also, you don't upload bigbed files to UCSC, you have to have them on your own server and provide a URL to UCSC to access them.
bigbed: http://genome.ucsc.edu/goldenPath/help/bigBed.html
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Old 04-15-2011, 07:47 AM   #7
poisson200
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Thank you for your answers

Quote:
Originally Posted by biznatch View Post
Also, you don't upload bigbed files to UCSC, you have to have them on your own server and provide a URL to UCSC to access them.
bigbed: http://genome.ucsc.edu/goldenPath/help/bigBed.html
Sorry, I knew this; I already use bb's but was lazy in precisely conveying it.

OK, I will try out your suggestions. Thanks.

Kind regards,

John.

Update;
Great, all is good with 10Mb gzip-ed into browser. thanks.

Last edited by poisson200; 04-15-2011 at 08:00 AM. Reason: Update; good news
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Old 02-20-2012, 10:19 AM   #8
earonesty
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Not cufflinks specific, and properly joins exons into one line, and annotates the "thick" and "thin" regions correctly (using start/stop codons if available)

http://code.google.com/p/ea-utils/so...lipper/gtf2bed
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