User: jms1223

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jms12230
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Posts by jms1223

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Comment: C: Exporting normalized counts over final DB windows from csaw
... My gut tells me that combining 4 samples will hinder your power to detect those "boundary" type peaks to begin with. But worse, "boundary" in this instance may mean not just weaker sites, but also those that exhibit meaningful variability across experimental conditions. In my experience, adding more ...
written 21 months ago by jms12230
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Comment: C: Exporting normalized counts over final DB windows from csaw
... This is perfect, thanks! ...
written 21 months ago by jms12230
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Comment: C: Exporting normalized counts over final DB windows from csaw
... I've been calling peaks relative to input controls, with biological duplicate on everything. So in other words I have Condition1, rep1 Condition1, rep2 Condition2, rep1 Condition2, rep2 Condition1, input rep1 Condition1, input rep2 Condition2, input rep1 Condition2, input rep2 So you wou ...
written 21 months ago by jms12230
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Comment: C: Exporting normalized counts over final DB windows from csaw
... Running regionCounts() seemed like the most direct approach to me, so I went with that. The values seem to be integers though, so I'm guessing these are raw counts based on reads pulled from the BAM files. Do I just scale these values by normfacs, or is that incorrect? Also if you can just sanity c ...
written 21 months ago by jms12230
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Comment: C: Exporting normalized counts over final DB windows from csaw
... Thanks for the reply. It seems like in this instance, cpm(y) provides those counts for all windows, rather than just the final merged/significant ones...though it's hard to tell since cpm(y) doesn't by default give me any row names. How would I get counts for the final windows, and annotate them wit ...
written 21 months ago by jms12230
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Exporting normalized counts over final DB windows from csaw
... I've successfully run csaw and identified windows with significantly different ChIP-seq enrichment across my experimental conditions. Instead of producing the genome browser-like plots outlined in the user manual, I would simply like to export the total (or ideally, mean per base) number of reads, s ...
edger chip-seq csaw written 21 months ago by jms12230 • updated 21 months ago by Ryan C. Thompson7.3k

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