[Gerritsen, M (onco)]

Dear reader,

 

I get the following error when trying to upload a file directly from GEO. Does this mean the file is to big and needs to be converted to a BigWig?

 

Thanks in advance,

 

Mylene Gerritsen

 

 

 

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[Brian Lee]

Dear Mylene,

Thank you for using the UCSC Genome Browser and your question about the memory limit error you are seeing.

You are correct that the path to take is to make a bigWig out of such files. To do so you would need the properly compiled wigToBigWig utility for your system. You can do "uname -a" and pick the utility from the matching directory here: http://hgdownload.soe.ucsc.edu/admin/exe/

Once you download the wigToBigWig utility you would also need to get the chrom.sizes file for the matching assembly, in this case mm8. You can obtain it here: http://hgdownload.cse.ucsc.edu/goldenPath/mm8/bigZips/mm8.chrom.sizes

Then one would normally run the utility with this command on the obtained unzipped wig file:
wigToBigWig GSM721212.wig mm8.chrom.sizes GSM721212.bigWig

However, this file has some errors, the first of which is there are some annotations that extend past the end of chromosomes, so you can avoid that problem using the -clip option, to clip these final entries:
wigToBigWig -clip GSM721212.wig mm8.chrom.sizes GSM721212.bigWig

The file also has some errors where "start=0" needs to be changed to "start=1", an example is line 86094512 for chrM: fixedStep chrom=chrM start=0 step=25 span=25

Please take these steps yourself for future files, but for your convenience I put these together here: http://hgwdev.cse.ucsc.edu/~brianlee/customTracks/GSM721212.txt

These tracks can be loaded with this URL: http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&hgt.customText=http://hgwdev.cse.ucsc.edu/~brianlee/customTracks/GSM721212.txt

Note that you can upload sections of the wig file, if for example you were only interested in chrM data, you could upload just that section and avoid the memory problem. However, the best solution is to create a bigWig file and host it in a publicly accessible directory. More about bigWig files can be found here: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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