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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