Bed to GTF file conversion

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meharji arumilli

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Jul 21, 2014, 12:15:43 PM7/21/14

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Hi,

I tried using the following scripts to convert bed file to GTF file which are available at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

bedToGenePred input.bed stdout | genePredToGtf -utr file stdin output.gtf

I have used the genePredToGtf script with -utr option to add 5UTR and 3UTR features. However, the output doesn't have the UTR features in the final GTF file irrespective of -utr option.

Could it be a bug in the script? Could someone give any ideas/suggestions to achieve this.

Best Regards
Mehar

Luvina Guruvadoo

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Jul 22, 2014, 9:56:06 AM7/22/14

to meharji arumilli, gen...@soe.ucsc.edu

Hello Meharji,

Thanks for your question. May I ask what your bed file looks like? Do you have the UTRs defined in your bed file? Please feel free to send us a few sample lines so we can take a closer look. You may send this information directly to me to avoid sharing it with the entire list.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group