possible --call-troughs functionality

[Xi Chen]

Hi Tao,

macs2 callpeak subcommand has an optional flag --call-summits. When enabled, it returns multiple summits (local maximum) within the same peak region. That is very helpful to get the exact binding site of your protein of interest.

However, when doing histone ChIP-seq, we not only cares about where histones are located but also want to look at the potential TF binding regions at the same time, which are often the trough regions within the histone chip-seq peak. This is one example:

In addition, when doing histone chip-seq, if you want to search to TF motifs, it is actually beneficial to just use the trough regions where TFs can bind to do the motif discovery.

Could you implement a --call-troughs option as well?

At the moment, I'm simply using the --call-summits to get the summits, and use the middle point of two summits as the trough, which is not ideal.

Thanks.

Regards,

Xi

[Ian Donaldson]

This would be a very useful feature.  The only other software I am aware of that does this is MUSIC (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234855/), but I personally found this quite challenging to run.

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[Xi Chen]

Thanks, Ian.

HOMER's findPeak also has this function (-nfr flag), but I have not personally tried it, so not sure.

Xi

On Wednesday, 9 November 2016 15:23:03 UTC, Ian wrote:

This would be a very useful feature.  The only other software I am aware of that does this is MUSIC (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234855/), but I personally found this quite challenging to run.

On 9 November 2016 at 15:06, Xi Chen <dbr...@gmail.com> wrote:

Hi Tao,

macs2 callpeak subcommand has an optional flag --call-summits. When enabled, it returns multiple summits (local maximum) within the same peak region. That is very helpful to get the exact binding site of your protein of interest.

However, when doing histone ChIP-seq, we not only cares about where histones are located but also want to look at the potential TF binding regions at the same time, which are often the trough regions within the histone chip-seq peak. This is one example:

In addition, when doing histone chip-seq, if you want to search to TF motifs, it is actually beneficial to just use the trough regions where TFs can bind to do the motif discovery.

Could you implement a --call-troughs option as well?

At the moment, I'm simply using the --call-summits to get the summits, and use the middle point of two summits as the trough, which is not ideal.

Thanks.

Regards,

Xi

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