Dataset formats

The input is in GFF format, and the output is tabular. (Dataset missing?)

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What it does

PASS (Poisson Approximation for Statistical Significance) detects significant transcription factor binding sites in the genome from ChIP data. This is probably the only peak-calling method that accurately controls the false-positive rate and FDR in ChIP data, which is important given the huge discrepancy in results obtained from different peak-calling algorithms. At the same time, this method achieves a similar or better power than previous methods.

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Hints

• ChIP-Seq data:

  If the data is from ChIP-Seq, you need to convert the ChIP-Seq values into z-scores before using this program. It is also recommended that you group read counts within a neighborhood together, e.g. in tiled windows of 30bp. In this way, the ChIP-Seq data will resemble ChIP-chip data in format.

• Choosing window size options:

  The window size is related to the probe tiling density. For example, if the probes are tiled at every 100bp, then setting the smallest window = 2 and largest window = 6 is appropriate, because the DNA fragment size is around 300-500bp.

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Example

• input file:

  chr7  Nimblegen  ID  40307603  40307652  1.668944     .  .  .
  chr7  Nimblegen  ID  40307703  40307752  0.8041307    .  .  .
  chr7  Nimblegen  ID  40307808  40307865  -1.089931    .  .  .
  chr7  Nimblegen  ID  40307920  40307969  1.055044     .  .  .
  chr7  Nimblegen  ID  40308005  40308068  2.447853     .  .  .
  chr7  Nimblegen  ID  40308125  40308174  0.1638694    .  .  .
  chr7  Nimblegen  ID  40308223  40308275  -0.04796628  .  .  .
  chr7  Nimblegen  ID  40308318  40308367  0.9335709    .  .  .
  chr7  Nimblegen  ID  40308526  40308584  0.5143972    .  .  .
  chr7  Nimblegen  ID  40308611  40308660  -1.089931    .  .  .
  etc.
  

  In GFF, a value of dot '.' is used to mean "not applicable".

• output file:

  ID  Chr   Start     End       WinSz  PeakValue  # of FPs  FDR
  1   chr7  40310931  40311266  4      1.663446   0.248817  0.248817
  

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References

Zhang Y. (2008) Poisson approximation for significance in genome-wide ChIP-chip tiling arrays. Bioinformatics. 24(24):2825-31. Epub 2008 Oct 25.

Chen KB, Zhang Y. (2010) A varying threshold method for ChIP peak calling using multiple sources of information. Submitted.