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Old 01-24-2011, 10:03 AM   #1
chrisbala
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Default visualizing scripture output BED

Hi,

I'm working through an analysis with Scripture for the first time.

I've been able to generate a bed and dot file. UCSC does not seem like this BED file.

I was able to find this suggestion that scripture includes a gff converter:

http://molecularevolution.org/resour...pture_activity

java -Xmx1000m -jar <path_to_scripture>/scripture.jar -task toGFF -cufflinks -in scripture.t0.bed -source SCRIPTURE -out scripture.t0.gtf -prefix t0

but... this toGFF function does not seem to be described in the scripture documentation, and does not seem to work for me either.

Any suggestions? All I am really trying to do is to get this into UCSC so I can quickly assess how things look. Scripture suggests IGV browser which I suppose I could also use.

thanks!
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Old 01-24-2011, 06:37 PM   #2
biznatch
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What happens when you try upload the .bed file to the UCSC browser?
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Old 01-25-2011, 09:23 AM   #3
chrisbala
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Default error message

I get this:

Code:
File 'allScores.bed' - Unrecognized format line 1 of custom track: chr1	199	249	chr1:199-249	0.0	*	199	249	0,0,0	1	50,	0,	1.0	0.3684297339584846	1.0	0.02 3.1075660687968516	0.0542844351489113	50.0	1.0 (note: chrom names are case sensitive)
thoughts? Maybe I need some sort of header?

generally the scripture documentation seems somewhat half written, unless I am missing something?
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Old 01-25-2011, 09:24 AM   #4
chrisbala
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fyi, the chromosome name is fine... (no caps problem there)
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Old 01-26-2011, 04:54 AM   #5
Emilie
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Hi,

I have been able to open bed files in UCSC Genome browser using Scripture-beta2 version and this type of command:

java -Xmx2000m -jar scripture-beta2.jar -task extractDot -in Segmentation_Results/chr1.scriptureESTest.segments.graph.post.add.pairs.dot -chr chr1 -start 6235241 -end 6239548 -out chr1_6235241-6239548.dot

It gives a dot file and a bed file for the indicated region of the chromosome.
Hope this help !

Emilie

Last edited by Emilie; 01-26-2011 at 04:57 AM.
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Old 01-27-2011, 08:16 AM   #6
biznatch
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.bed files don't require a header, but you can include one. Bed format instructions:
http://genome.ucsc.edu/FAQ/FAQformat#format1
I think you have too many columns in your file. Can you post the first few lines from your file, exactly as written in the file?
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Old 12-06-2013, 11:05 AM   #7
11xinqi
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Quote:
Originally Posted by chrisbala View Post
Hi,

I'm working through an analysis with Scripture for the first time.

I've been able to generate a bed and dot file. UCSC does not seem like this BED file.

I was able to find this suggestion that scripture includes a gff converter:

http://molecularevolution.org/resour...pture_activity

java -Xmx1000m -jar <path_to_scripture>/scripture.jar -task toGFF -cufflinks -in scripture.t0.bed -source SCRIPTURE -out scripture.t0.gtf -prefix t0

but... this toGFF function does not seem to be described in the scripture documentation, and does not seem to work for me either.

Any suggestions? All I am really trying to do is to get this into UCSC so I can quickly assess how things look. Scripture suggests IGV browser which I suppose I could also use.

thanks!
Would you tell me that how can you transfer the bed file from scripture to gtf file please?
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