How to display biological replicates in a single UCSC track

LP_SEP23 · 10-09-2012, 08:07 AM

Hi All,

I have ChIP-seq experiment with 2 conditions and 9 biological replicates on each
I have no problem displaying the alignments for each replicate (usually as bigWig). Looking at replicates individually can be a little misleading, so I wanted to create a track that displays the average among replicates and I am not sure what is the best way to do it.

Should I just scan the genome (mouse) at some defined window and take the average of coverage per window after correcting by library depth? or should I do per-base coverage?
Will it be better to combine all the reads from all the replicates and generate a single merged file?
Is there any utility already available to do this?

thanks very much for the help

Lucia

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10-09-2012, 08:07 AM	#1
LP_SEP23 Junior Member Location: Philadelphia Join Date: Feb 2012 Posts: 9	How to display biological replicates in a single UCSC track Hi All, I have ChIP-seq experiment with 2 conditions and 9 biological replicates on each I have no problem displaying the alignments for each replicate (usually as bigWig). Looking at replicates individually can be a little misleading, so I wanted to create a track that displays the average among replicates and I am not sure what is the best way to do it. Should I just scan the genome (mouse) at some defined window and take the average of coverage per window after correcting by library depth? or should I do per-base coverage? Will it be better to combine all the reads from all the replicates and generate a single merged file? Is there any utility already available to do this? thanks very much for the help Lucia