[Gmod-ajax] index transcript_id?

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[Gmod-ajax] index transcript_id?

Sofia Robb
Hi,

Is there a way to get generate_names.pl to index the name as well as the transcript_id value which is found in the 9th column of my gff? 

Thanks!
Sofia

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Re: index transcript_id?

Colin
You can use --nameAttributes with flatfile-to-json.pl to give a list of attributes that you want to index from your GFF e.g. flatfile-to-json.pl --nameAttributes "transcript_id,name,other_gff_column9_field,id" etc

After you use this, then generate-names.pl will pick up this value. It is sort of confusing that it requires special input at the flatfile-to-json.pl level and not the generate-names.pl level, but hopefully that helps.


-Colin

On Mon, Nov 28, 2016 at 3:57 PM, Sofia Robb <[hidden email]> wrote:
Hi,

Is there a way to get generate_names.pl to index the name as well as the transcript_id value which is found in the 9th column of my gff? 

Thanks!
Sofia

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Re: index transcript_id?

Sofia Robb
Great! I was thinking that I might have to load with flatfile-to-jason differently for this to work, but wasn't exactly sure. This is perfect!!

Thank you Colin,
Sofia



On Mon, Nov 28, 2016 at 2:24 PM, Colin <[hidden email]> wrote:
You can use --nameAttributes with flatfile-to-json.pl to give a list of attributes that you want to index from your GFF e.g. flatfile-to-json.pl --nameAttributes "transcript_id,name,other_gff_column9_field,id" etc

After you use this, then generate-names.pl will pick up this value. It is sort of confusing that it requires special input at the flatfile-to-json.pl level and not the generate-names.pl level, but hopefully that helps.


-Colin

On Mon, Nov 28, 2016 at 3:57 PM, Sofia Robb <[hidden email]> wrote:
Hi,

Is there a way to get generate_names.pl to index the name as well as the transcript_id value which is found in the 9th column of my gff? 

Thanks!
Sofia

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