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104 lines
2.9 KiB
XML
104 lines
2.9 KiB
XML
<tool id="cshl_fasta_clipping_histogram" name="Length Distribution">
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<description>chart</description>
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<command>fasta_clipping_histogram.pl $input $outfile</command>
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<inputs>
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<param format="fasta" name="input" type="data" label="Library to analyze" />
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</inputs>
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<outputs>
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<data format="png" name="outfile" metadata_source="input" />
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</outputs>
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<help>
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**What it does**
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This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
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**TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
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-----
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**Output Examples**
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In the following library, most sequences are 24-mers to 27-mers.
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This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
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.. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png
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In the following library, most sequences are 19,22 or 23-mers.
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This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
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.. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png
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-----
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**Input Formats**
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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::
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>sequence1
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AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
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>sequence2
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GTGTGTGTGGGAAGTTGACACAGTA
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>sequence3
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CCTTGAGATTAACGCTAATCAAGTAAAC
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If the sequences span over multiple lines::
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>sequence1
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CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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aactggtctttacctTTAAGTTG
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Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
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>sequence1
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CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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-----
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**Multiplicity counts (a.k.a reads-count)**
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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).
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Example 1 - The following FASTA file *does not* have multiplicity counts::
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>seq1
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GGATCC
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>seq2
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GGTCATGGGTTTAAA
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>seq3
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GGGATATATCCCCACACACACACAC
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Each sequence is counts as one, to produce the following chart:
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.. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png
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Example 2 - The following FASTA file have multiplicity counts::
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>seq1-2
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GGATCC
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>seq2-10
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GGTCATGGGTTTAAA
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>seq3-3
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GGGATATATCCCCACACACACACAC
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The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
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.. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png
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Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
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</help>
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</tool>
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<!-- FASTA-Clipping-Histogram is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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