0
|
1 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution">
|
|
2 <description>chart</description>
|
|
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
|
|
4 <command>fasta_clipping_histogram.pl $input $outfile</command>
|
|
5
|
|
6 <inputs>
|
|
7 <param format="fasta" name="input" type="data" label="Library to analyze" />
|
|
8 </inputs>
|
|
9
|
|
10 <outputs>
|
|
11 <data format="png" name="outfile" metadata_source="input" />
|
|
12 </outputs>
|
|
13 <help>
|
|
14
|
|
15 **What it does**
|
|
16
|
|
17 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
|
|
18
|
|
19 **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
|
|
20
|
|
21 -----
|
|
22
|
|
23 **Output Examples**
|
|
24
|
|
25 In the following library, most sequences are 24-mers to 27-mers.
|
|
26 This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
|
|
27
|
|
28 .. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png
|
|
29
|
|
30
|
|
31 In the following library, most sequences are 19,22 or 23-mers.
|
|
32 This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
|
|
33
|
|
34 .. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png
|
|
35
|
|
36
|
|
37 -----
|
|
38
|
|
39
|
|
40 **Input Formats**
|
|
41
|
|
42 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::
|
|
43
|
|
44 >sequence1
|
|
45 AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
|
|
46 >sequence2
|
|
47 GTGTGTGTGGGAAGTTGACACAGTA
|
|
48 >sequence3
|
|
49 CCTTGAGATTAACGCTAATCAAGTAAAC
|
|
50
|
|
51
|
|
52 If the sequences span over multiple lines::
|
|
53
|
|
54 >sequence1
|
|
55 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
|
|
56 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
|
|
57 aactggtctttacctTTAAGTTG
|
|
58
|
|
59 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
|
|
60
|
|
61 >sequence1
|
|
62 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
|
|
63
|
|
64
|
|
65 -----
|
|
66
|
|
67
|
|
68
|
|
69 **Multiplicity counts (a.k.a reads-count)**
|
|
70
|
|
71 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).
|
|
72
|
|
73 Example 1 - The following FASTA file *does not* have multiplicity counts::
|
|
74
|
|
75 >seq1
|
|
76 GGATCC
|
|
77 >seq2
|
|
78 GGTCATGGGTTTAAA
|
|
79 >seq3
|
|
80 GGGATATATCCCCACACACACACAC
|
|
81
|
|
82 Each sequence is counts as one, to produce the following chart:
|
|
83
|
|
84 .. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png
|
|
85
|
|
86
|
|
87 Example 2 - The following FASTA file have multiplicity counts::
|
|
88
|
|
89 >seq1-2
|
|
90 GGATCC
|
|
91 >seq2-10
|
|
92 GGTCATGGGTTTAAA
|
|
93 >seq3-3
|
|
94 GGGATATATCCCCACACACACACAC
|
|
95
|
|
96 The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
|
|
97
|
|
98 .. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png
|
|
99
|
|
100 Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
|
|
101
|
|
102 </help>
|
|
103 </tool>
|
|
104 <!-- FASTA-Clipping-Histogram is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
|