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tRNA and rRNA features being incorrectly added using generate_encoded_features function #3

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ncbk opened this Issue Feb 10, 2013 · 3 comments

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ncbk commented Feb 10, 2013

when using: genomer view table --generate_encoded_features

tRNA and rRNA features are added as a CDS features. Is there a way to add tRNA and rRNA as the correct feature (i.e. as rRNA and tRNA features)?

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michaelbarton commented Feb 11, 2013

Adding feature_type=rRNA or feature_type=tRNA to the ninth column of your gff file should generate these features. Please write back if this doesn't work.

ncbk commented Feb 11, 2013

I'm currently creating my gff file using a genbank file and the bio perl script bp_genbank2gff3.pl. I don't believe there is a function in this script to add the feature_type in the 9th column. How do you create your gff files? Alternatively I could write a script to make the required changes to the gff but I'm wondering if you have a more direct fix.

Thanks,
Natalie Knox

On 2013-02-11, at 8:32 AM, Michael Barton notifications@github.com wrote:

Adding feature_type=rRNA or feature_type=tRNA to the ninth column of your gff file should generate these features. Please write back if this doesn't work.


Reply to this email directly or view it on GitHub..

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michaelbarton commented Feb 11, 2013

Could you provide more information on what you're aiming to do? What is the source of the Genbank file?

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