Question: Bedgraph Size Limit Upload to UCSC
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gravatar for virlana.shchuka
11 months ago by
virlana.shchuka0 wrote:

I have some ChIP-seq and RNA-seq datasets that are too big for uploading to UCSC. Is there a way to compress these datasets and upload compressed versions? I currently have my other datasets uploaded in bedgraph format, so it would be optimal if I didn't have to convert the too large bedgraphs to a different file type.

rna-seq chip-seq • 430 views
ADD COMMENTlink modified 11 months ago by ATpoint14k • written 11 months ago by virlana.shchuka0
0
gravatar for ATpoint
11 months ago by
ATpoint14k
Germany
ATpoint14k wrote:

I personally prefer the bigwig format. You can get it from your bedGraph via bedGraphToBigwig, which is part of kentUtils. If you want to keep using UCSC browser, you'll have to upload the bigwig somewhere on your webserver and provide the link to UCSC. Check the UCSC documentation for details on that.

ADD COMMENTlink modified 11 months ago • written 11 months ago by ATpoint14k

Thank you, ATpoint! I will take a look, although I would like to maintain the bedgraph file type, if possible. I did try uploading a gzipped version of the bedgraph, which seems to work okay - can you confirm if this is 'sound'?

ADD REPLYlink written 11 months ago by virlana.shchuka0
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