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comparison tools/human_genome_variation/pass.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="hgv_pass" name="PASS" version="1.0.0">
2 <description>significant transcription factor binding sites from ChIP data</description>
3
4 <command interpreter="bash">
5 pass_wrapper.sh "$input" "$min_window" "$max_window" "$false_num" "$output"
6 </command>
7
8 <inputs>
9 <param format="gff" name="input" type="data" label="Dataset"/>
10 <param name="min_window" label="Smallest window size (by # of probes)" type="integer" value="2" />
11 <param name="max_window" label="Largest window size (by # of probes)" type="integer" value="6" />
12 <param name="false_num" label="Expected total number of false positive intervals to be called" type="float" value="5.0" help="N.B.: this is a &lt;em&gt;count&lt;/em&gt;, not a rate." />
13 </inputs>
14
15 <outputs>
16 <data format="tabular" name="output" />
17 </outputs>
18
19 <requirements>
20 <requirement type="package">pass</requirement>
21 <requirement type="binary">sed</requirement>
22 </requirements>
23
24 <!-- we need to be able to set the seed for the random number generator
25 <tests>
26 <test>
27 <param name="input" ftype="gff" value="pass_input.gff"/>
28 <param name="min_window" value="2"/>
29 <param name="max_window" value="6"/>
30 <param name="false_num" value="5"/>
31 <output name="output" file="pass_output.tab"/>
32 </test>
33 </tests>
34 -->
35
36 <help>
37 **Dataset formats**
38
39 The input is in GFF_ format, and the output is tabular_.
40 (`Dataset missing?`_)
41
42 .. _GFF: ./static/formatHelp.html#gff
43 .. _tabular: ./static/formatHelp.html#tab
44 .. _Dataset missing?: ./static/formatHelp.html
45
46 -----
47
48 **What it does**
49
50 PASS (Poisson Approximation for Statistical Significance) detects
51 significant transcription factor binding sites in the genome from
52 ChIP data. This is probably the only peak-calling method that
53 accurately controls the false-positive rate and FDR in ChIP data,
54 which is important given the huge discrepancy in results obtained
55 from different peak-calling algorithms. At the same time, this
56 method achieves a similar or better power than previous methods.
57
58 <!-- we don't have wrapper support for the "prior" file yet
59 Another unique feature of this method is that it allows varying
60 thresholds to be used for peak calling at different genomic
61 locations. For example, if a position lies in an open chromatin
62 region, is depleted of nucleosome positioning, or a co-binding
63 protein has been detected within the neighborhood, then the position
64 is more likely to be bound by the target protein of interest, and
65 hence a lower threshold will be used to call significant peaks.
66 As a result, weak but real binding sites can be detected.
67 -->
68
69 -----
70
71 **Hints**
72
73 - ChIP-Seq data:
74
75 If the data is from ChIP-Seq, you need to convert the ChIP-Seq values
76 into z-scores before using this program. It is also recommended that
77 you group read counts within a neighborhood together, e.g. in tiled
78 windows of 30bp. In this way, the ChIP-Seq data will resemble
79 ChIP-chip data in format.
80
81 - Choosing window size options:
82
83 The window size is related to the probe tiling density. For example,
84 if the probes are tiled at every 100bp, then setting the smallest
85 window = 2 and largest window = 6 is appropriate, because the DNA
86 fragment size is around 300-500bp.
87
88 -----
89
90 **Example**
91
92 - input file::
93
94 chr7 Nimblegen ID 40307603 40307652 1.668944 . . .
95 chr7 Nimblegen ID 40307703 40307752 0.8041307 . . .
96 chr7 Nimblegen ID 40307808 40307865 -1.089931 . . .
97 chr7 Nimblegen ID 40307920 40307969 1.055044 . . .
98 chr7 Nimblegen ID 40308005 40308068 2.447853 . . .
99 chr7 Nimblegen ID 40308125 40308174 0.1638694 . . .
100 chr7 Nimblegen ID 40308223 40308275 -0.04796628 . . .
101 chr7 Nimblegen ID 40308318 40308367 0.9335709 . . .
102 chr7 Nimblegen ID 40308526 40308584 0.5143972 . . .
103 chr7 Nimblegen ID 40308611 40308660 -1.089931 . . .
104 etc.
105
106 In GFF, a value of dot '.' is used to mean "not applicable".
107
108 - output file::
109
110 ID Chr Start End WinSz PeakValue # of FPs FDR
111 1 chr7 40310931 40311266 4 1.663446 0.248817 0.248817
112
113 -----
114
115 **References**
116
117 Zhang Y. (2008)
118 Poisson approximation for significance in genome-wide ChIP-chip tiling arrays.
119 Bioinformatics. 24(24):2825-31. Epub 2008 Oct 25.
120
121 Chen KB, Zhang Y. (2010)
122 A varying threshold method for ChIP peak calling using multiple sources of information.
123 Submitted.
124
125 </help>
126 </tool>