Bedgraph Size Limit Upload to UCSC

Question

[virlana.shchuka]

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.

Answer 1

[ATpoint]

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.

[virlana.shchuka]

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'?