Uncertainty over the use of -b (--bg) parameter

[gilless429]

Hello, I am having a bit a of problem with the above-mentionned -b parameter.

I apologize if this is not strictly appropriate use of the git issue system, but as I tried asking questions over at the relevant google group for DANPOS and did not get a response, I thought I would try my luck here.

I am using ChIP-seq data and would like to know if the -b parameter can/should be used to provide the ChIP-seq input (by which I mean the results for a sample just like the IP, except it does not undergo immunoprecipitation). After reading the documentation on this parameter I am sadly still uncertain.

Thanks in advance for any help you can provide,
Gilles

[SimHolz]

For completeness here my answer in the google group:

Hi Gilles,

First I am not the original developer of the program and although I used it a lot and went through quite a lot of the source code I still do not understand every aspect of it. So here are just some of my thoughts

1. The -bg parameter does the following: The bg input gets smoothed (smoothing window is controlled by -l/-lmd) and then subtracted from all samples. This leads to a kind of "soft" background removal, which means you will still find peaks if you use the -bg with the same data as the input. The parameter has its use but I would be careful. Maybe have a few tries and see if the result is what you want/expect.

2. The -c parameter can be used for read-count normalisation between samples. But If you know the ratios between your samples from your spike in you can use it to normalise to those ratios as well.

3. I do it the exact same way, you are planning to do. Just one remark: DANPOS will only pool the replicates and not do any statistics with those.

Bw
Simon