Uploading Large GFF files

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Uploading Large GFF files

Christopher Barrington

I have several large GFF files from Illumina experiments. Each GFF contains over 1 million features. When I load this GFF into my mySQL database using

bp_seqfeature_load.pl -c -f -u X -p X -d IlluminaData smRNA*

the process takes a very long time to load the files. I checked the mySQL processlist and it shows that the load query is using a 'replace into' clause. Is this the reason that the script takes so long to load a file, if so is there a work-around (other than making a new database for each experiment)? Naive question: is there any sense in using replace into since the primary key is set to auto-increment?

Many thanks,

- Christopher

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