Hi Lee, If you have BAM from your Illumina sequencing run, and can put .bam and .bai (index) files on a web server, then we can display the BAM as a custom track by fetching only the parts of the file that are needed for display. Instructions are here:
http://genome.ucsc.edu/goldenPath/help/bam.html Since you have paired-end data, I recommend adding the "pairEndsByName=." setting described there. If you have more questions, please send them to us at [email protected] . Angie ----- Original Message ----- > From: "Lee Edsall" <[email protected]> > To: "Hiram Clawson" <[email protected]> > Cc: [email protected] > Sent: Wednesday, March 14, 2012 2:38:36 PM > Subject: Re: [Genome] Question about GFF file sizes > 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 > >> > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
