genome descriptive statistics

dnusol · 04-13-2012, 03:27 AM

Hi there!

apart from number of reads aligning and mean coverage after alignment, what other things are interesting to evaluate to see if a WGA experiment is gone OK?
for example, how can I evaluate whether I have long runs of zero coverage? is it possible to see alignment bias? I am not sure if it would be possible to get that just from visual inspection of all human chromosomes for example. Some kind of metrics or statistics or general graph.

Maybe dot plots are relevant in this case but how can it be done for a whole genome? I don't need comparison between genomes, but just evaluation of one sequenced genome

Thanks,

D.

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04-13-2012, 03:27 AM	#1
dnusol Senior Member Location: Spain Join Date: Jul 2009 Posts: 133	genome descriptive statistics Hi there! apart from number of reads aligning and mean coverage after alignment, what other things are interesting to evaluate to see if a WGA experiment is gone OK? for example, how can I evaluate whether I have long runs of zero coverage? is it possible to see alignment bias? I am not sure if it would be possible to get that just from visual inspection of all human chromosomes for example. Some kind of metrics or statistics or general graph. Maybe dot plots are relevant in this case but how can it be done for a whole genome? I don't need comparison between genomes, but just evaluation of one sequenced genome Thanks, D. Last edited by dnusol; 04-13-2012 at 03:29 AM.