Question: Comparison of bamCoverage log2 ratios in deeptools
gravatar for ATpoint
28 days ago by
ATpoint3.2k wrote:

Is anyone experienced in using bamCompare from deeptools? I ran it to compare a ChIP sample to its input, using SES normalization, outputting the log2 ratio. If I do the same on a replicate with its own input, can I then directly compare the log2 ratios for the two outputs in a certain region (or the genome), e.g. for a sample-to-sample correlation plot?

bamCompare -e 200 -bs 1 --scaleFactorsMethod SES -o out_log2ratio.bigwig -b1 sample.bam -b2 input.bam
ADD COMMENTlink modified 28 days ago by Devon Ryan77k • written 28 days ago by ATpoint3.2k
gravatar for Devon Ryan
28 days ago by
Devon Ryan77k
Freiburg, Germany
Devon Ryan77k wrote:

Yes, you can directly compare the SES normalized replicates. Keep in mind that you're then looking at not only the difference in signal distribution between the replicates, but also how well those replicates were enriched relative to their inputs. In general, SES makes sharper marks more distinct (this is good), but if you have either a poorer enrichment in one sample or a weird input sample then you might get a bit poorer comparison than otherwise.

ADD COMMENTlink modified 28 days ago • written 28 days ago by Devon Ryan77k
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