BED files for GREAT program

[Archibald Perkins]

Hi,

we received a .bed file for a ChIP experiment and want to use the Stanford GREAT program (http://bejerano.stanford.edu/great/public/html/) to generate a list of genes located near the transcription factor binding sites. However, the GREAT program only allows .bed files up to 50 megabytes, and our data is 1200 megabytes (not sure why it is so big).

Is it possible to use the QuEST program to generate a list similar to that provided by the GREAT program?

Or, is it possible to use QuEST program to generate a smaller .bed file that can then be uploaded into the GREAT program?

Thanks.

[Anton]

Hi Archibald, can you please paste a few lines from your bed files?

Use 

head -10 yourfile.bed

[Hunter Richards]

How many lines of data is it? There might be too many genomic sites in your file to generate any output since you might hit most or all the genes in the genome. That's happened to me before, and the bed file wasn't anywhere near 50 MB.

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[Archibald Perkins]

I am having trouble opening it!

[Anton]

To see the first 10 lines try this:

head -10 yourfile.bed

To count the number of lines

wc -l yourfile.bed