[Bioperl-l] Problem with parsing ENSEMBL genbank flat file wi th genbank2gff3. pls

[Babenko, Vladimir (NIH/NLM/NCBI)]

    Sorry Ewan, 
Now I got that when I check multiple transcripts  it means genes with no
less than 2 transcripts.
     The Mart is amazing.
    Regards,
	Vladimir

>-----Original Message-----
>From: Ewan Birney [mailto:birney at ebi.ac.uk] 
>Sent: Tuesday, January 18, 2005 1:35 PM
>To: Babenko, Vladimir (NIH/NLM/NCBI)
>Cc: 'cjm at fruitfly.org'; 'cain at cshl.edu'; 'jason.stajich at duke.edu'
>Subject: RE: [Bioperl-l] Problem with parsing ENSEMBL genbank 
>flat file wi th genbank2gff3. pls
>
>On Tue, 18 Jan 2005, Babenko, Vladimir (NIH/NLM/NCBI) wrote:
>
>>        Hi all,
>> Thank you for your prompt response:
>> I believe that gff* is one of the ways to manage data, so 
>this is the 
>> reason I'm up to this.
>>      I played around for a while with all you propositions, 
>so further 
>> is a short response:
>> 1) Chris - I checked the script, it works fine, thank you. I'm 
>> currently exploring this option.
>> The point is that I do need to have both mRNA and CDS linked 
>to check 
>> for UTR, introns, and looks like genbank2gff3 works fine here.
>> 2) Ensmart - this is a great proposition. I haven't come to 
>the end of 
>> the investigation of this sound product, but it is my sneaky 
>suspicion 
>> that I need some kind of mysql dump to manage the stuff by myself in 
>> the same way bioperl does, but again it's a compromise between 
>> compexity and simplicity that I cannot fully embrace for a while.
>> Still the option of species comparison may annihilate my suspicions 
>> momentarily if I will be able to manage it.
>> BTW, Ewan, 'unchecking' for the entire genome and setting multiple 
>> transcripts for human yields (all other options unchecked) after 
>> Filters stage yields:
>> 7185 Entries pass Filters - that looks a bit few for human. 
>Probably I 
>> miss out something, sorry.
>
>You want to uncheck the "multiple transcripts" (this means 
>genes with more than one transcript: you want all genes).
>
>
>