Convert *.peak.sig.bed to narrowpeak format for IDR

[coy...@gmail.com]

Hi,

I'd like to try using the peak files I've generated for my recent experiment with the ENCODE IDR pipeline to generate a set of high confidence peaks. To be transparent, I'll point out that I haven't used IDR before.

IDR doc here: https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit

This requires peaks in a narrowpeak (BED 6+4) or broadpeak (BED 6+3) format.

narrowpeak: http://genome.ucsc.edu/FAQ/FAQformat.html#format12

broadpeak: http://genome.ucsc.edu/FAQ/FAQformat.html#format13

e.g. for broadpeak columns:

7. signalValue - Measurement of overall (usually, average) enrichment for the region.

8. pValue - Measurement of statistical significance (-log10). Use -1 if no pValue is assigned.

9. qValue - Measurement of statistical significance using false discovery rate (-log10). Use -1 if no qValue is assigned.

One line of a CTK peak.sig.bed contains the following:

chr1    865532  865548  Peak_1[gene=148398][PH=10][PH0=0.07][P=1.00e-100]       10      +

What is the most appropriate way to convert to broadpeak?

Perhaps signal value ought to be either:

1. CTK PH / PH0

2. Some normalization with the size-matched input could also be performed.

3. CTK PH raw

My inclination would be to try PH/PH0, but I am only so experienced with this, and therefore not so confident.

Also, would the CTK peak p-value be appropriate here to use in col. 8?

From there, I would assume it is a matter of informed preference for what input (signal value or p-value) you use for IDR ranking.

I welcome any insight and thanks for your time.

Kind regards,

Steve

[Chaolin Zhang]

I would recommend peak height for column 7, p-value for column 8 and FDR in column 9 (you will need to calculate based on the reported p-values).

Chaolin

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[coy...@gmail.com]

Hi Chaolin,

Thank you for the lightning fast reply!

I'll give it a shot.

Steve