Hiram,
Thank you for the quick reply.
The GFF file does have linked items. It's data from a paired-end
Illumina sequencing run so ideally I'd like to see read1 associated with
read2 (which will show me the whole DNA fragment). If I convert the
data to a bed file, I lose that association.
Alternatively, if it is a size issue, I can split the file into subfiles
and load them separately. What's the maximum size the files can be?
Thank you,
Lee
Received from Hiram Clawson on 3/14/12 2:19 PM:
> Good Afternoon Lee:
>
> Is your GFF file actually linked items where multiple lines in the GFF
> file
> have a common identifier to indicate the separate lines are part of
> the same
> feature ? Or is your GFF file merely a listing of separate items ?
>
> If your GFF file is simply separate items, you can turn it into a bed
> file
> by selecting out a couple of the columns. For example:
>
> $ awk '{print $1,$4,$5,$2,0,$7}' yourData.gff > yourData.bed
>
> Assuming column 2 is a meaningful name. If this is a large bed
> file, use the bedToBigBed converter and use the resulting big bed
> file at a URL for your custom track.
>
> --Hiram
>
> Lee Edsall wrote:
>> I have been trying to upload a GFF as a custom track and been
>> encountering errors. The errors are:
>>
>> Example 1:
>> Can't start query:
>> select genome from dbDb where name = 'hg19'
>> mySQL error 2008: MySQL client ran out of memory
>>
>> Example 2:
>> Couldn't connect to database hgcentral on genome-centdb as
>> hgcentuser.
>> MySQL client ran out of memory
>>
>> I get the errors regardless of whether I link to a website (I've
>> tried 2 different ones) or upload from my computer.
>>
>> Perhaps the file I am trying to upload is too large? It is 1.1mb
>> gzipped.
>>
>> Any suggestions would be appreciated.
>>
>> Thank you,
>> Lee Edsall
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>
>
>
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