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annotate fasta_clipping_histogram.xml @ 3:d0969fa24eb1 draft
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| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:38:50 -0400 |
| parents | de44f4045b05 |
| children | 40ec4170291e |
| rev | line source |
|---|---|
| 1 | 1 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0"> |
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2 <description>chart</description> |
| 0 | 3 <requirements> |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
| 5 </requirements> | |
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6 <command>fasta_clipping_histogram.pl $input $outfile</command> |
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7 |
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8 <inputs> |
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9 <param format="fasta" name="input" type="data" label="Library to analyze" /> |
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10 </inputs> |
| 0 | 11 |
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12 <outputs> |
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13 <data format="png" name="outfile" metadata_source="input" /> |
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14 </outputs> |
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15 <tests> |
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16 </tests> |
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17 <help> |
| 0 | 18 **What it does** |
| 19 | |
| 20 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file. | |
| 21 | |
| 22 **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results. | |
| 23 | |
| 24 ----- | |
| 25 | |
| 26 **Output Examples** | |
| 27 | |
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28 In the following library, most sequences are 24-mers to 27-mers. |
| 0 | 29 This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place). |
| 30 | |
| 31 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png | |
| 32 | |
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33 In the following library, most sequences are 19,22 or 23-mers. |
| 0 | 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 **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 If the sequences span over multiple lines:: | |
| 52 | |
| 53 >sequence1 | |
| 54 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG | |
| 55 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG | |
| 56 aactggtctttacctTTAAGTTG | |
| 57 | |
| 58 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences:: | |
| 59 | |
| 60 >sequence1 | |
| 61 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG | |
| 62 | |
| 63 ----- | |
| 64 | |
| 65 **Multiplicity counts (a.k.a reads-count)** | |
| 66 | |
| 67 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). | |
| 68 | |
| 69 Example 1 - The following FASTA file *does not* have multiplicity counts:: | |
| 70 | |
| 71 >seq1 | |
| 72 GGATCC | |
| 73 >seq2 | |
| 74 GGTCATGGGTTTAAA | |
| 75 >seq3 | |
| 76 GGGATATATCCCCACACACACACAC | |
| 77 | |
| 78 Each sequence is counts as one, to produce the following chart: | |
| 79 | |
| 80 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png | |
| 81 | |
| 82 Example 2 - The following FASTA file have multiplicity counts:: | |
| 83 | |
| 84 >seq1-2 | |
| 85 GGATCC | |
| 86 >seq2-10 | |
| 87 GGTCATGGGTTTAAA | |
| 88 >seq3-3 | |
| 89 GGGATATATCCCCACACACACACAC | |
| 90 | |
| 91 The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart: | |
| 92 | |
| 93 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png | |
| 94 | |
| 95 Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. | |
| 96 | |
| 97 ------ | |
| 98 | |
| 99 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 100 | |
| 101 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
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102 </help> |
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103 </tool> |