UCSC uploading error

[ssseq]

Hi everyone,

I'm getting an error trying to upload a GFF file to the UCSC genome browser. When I copy and paste a few lines of the file, it works fine so I know the file format is ok. When I try to do the whole file I get this error.
********
File 'splitetv2moab.gff' - track load error (track name='ct_UserTrack_3545'):
start -1, end 101 out of range in findBin (max is 512M)
********
There are no "-1"s in the file. I thought perhaps it was because the file was too big (118 MB- not that big in general); so I split it into 4 files, but that still isn't working.

Has anyone seen this error before or have any suggestions on how to get this file to upload?

Thanks,
Sarah

[biznatch]

I can't help with that error specifically, but the UCSC genome browser file size limit is 500mb and approx. 100million lines (although I've uploaded up to 200million). So file size probably isn't your problem. If the file is too big, it'll either tell you it's too big, over 500mb, or it will just time out and go to a blank screen.

[samanta]

Seems like your gff file has problems. The best way to sort it would be to partition the file into two parts and see whether each part loads fine. Trying first few lines does not help, if the error is in 6000th line or so.

BTW, when you partition the file, please try to make sure it does not split data from a gene into two parts. Partitioning along chromosomes or scaffolds works best.

[ssseq]

Thanks for the comments- I had actually tried that and still couldn't figure out why it didn't work. I ended up just converting to .bed format, which worked fine. Thanks for the help!