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comparison fasta_clipping_histogram.xml @ 0:f2ab5b44870d draft

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author devteam
date Wed, 25 Sep 2013 14:55:11 -0400
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1 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0">
2 <description>chart</description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>fasta_clipping_histogram.pl $input $outfile</command>
7
8 <inputs>
9 <param format="fasta" name="input" type="data" label="Library to analyze" />
10 </inputs>
11
12 <outputs>
13 <data format="png" name="outfile" metadata_source="input" />
14 </outputs>
15 <help>
16
17 **What it does**
18
19 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
20
21 **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
22
23 -----
24
25 **Output Examples**
26
27 In the following library, most sequences are 24-mers to 27-mers.
28 This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
29
30 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png
31
32
33 In the following library, most sequences are 19,22 or 23-mers.
34 This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
35
36 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png
37
38
39 -----
40
41
42 **Input Formats**
43
44 This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
45
46 >sequence1
47 AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
48 >sequence2
49 GTGTGTGTGGGAAGTTGACACAGTA
50 >sequence3
51 CCTTGAGATTAACGCTAATCAAGTAAAC
52
53
54 If the sequences span over multiple lines::
55
56 >sequence1
57 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
58 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
59 aactggtctttacctTTAAGTTG
60
61 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
62
63 >sequence1
64 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
65
66
67 -----
68
69
70
71 **Multiplicity counts (a.k.a reads-count)**
72
73 If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing).
74
75 Example 1 - The following FASTA file *does not* have multiplicity counts::
76
77 >seq1
78 GGATCC
79 >seq2
80 GGTCATGGGTTTAAA
81 >seq3
82 GGGATATATCCCCACACACACACAC
83
84 Each sequence is counts as one, to produce the following chart:
85
86 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png
87
88
89 Example 2 - The following FASTA file have multiplicity counts::
90
91 >seq1-2
92 GGATCC
93 >seq2-10
94 GGTCATGGGTTTAAA
95 >seq3-3
96 GGGATATATCCCCACACACACACAC
97
98 The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
99
100 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png
101
102 Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
103
104 ------
105
106 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
107
108 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
109
110 </help>
111 <!-- FASTA-Clipping-Histogram is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
112 </tool>