convert gtf to bed12
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7.3 years ago
Amy ▴ 20

Hi, I want to convert .gtf file to UCSC .bed(12) file.

E.g .bed file (12 columns)

chr1    11873    14409    u01a.3    0    +    11873    11873    0    3    354,109,1189,    0,739,1347,
chr1    11873    14409    u01n.1    0    +    12189    13639    0    3    354,127,1007,    0,721,1529,
chr1    11873    14409    u01x.1    0    +    11873    11873    0    3    354,52,1189,    0,772,1347,
chr1    14362    17765    u09s.2    0    -    14362    14362    0    4    467,69,147,159,    0,607,1433,2244,

I know it's an old topic, however I couldn't find a satisfied answer. I tried bedops gtf2bed, but the output .bed is not what I want. I also tried several perl and python script, none of them work.

Thank you in advance for any help!

gtf bed • 9.1k views
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Manvendra Singh answered this already in your previous post here. I don't think its a good idea to duplicate your posts.

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You asked this in your previous post too, have a look here

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Entering edit mode
7.3 years ago
Amy ▴ 20

Hi, I found a script which works perfectly on this question!

http://allaboutbioinfo.blogspot.se/2011/08/converting-cufflinks-gtf-predictions-to.html

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