Question: Comparison of bamCoverage log2 ratios in deeptools
0
gravatar for ATpoint
9 months ago by
ATpoint10k
Germany
ATpoint10k 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 9 months ago by Devon Ryan86k • written 9 months ago by ATpoint10k
2
gravatar for Devon Ryan
9 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k 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 9 months ago • written 9 months ago by Devon Ryan86k
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