<tool id="cshl_fasta_clipping_histogram" name="Length Distribution">
<command>fasta_clipping_histogram.pl $input $outfile</command>
<param format="fasta" name="input" type="data" label="Library to analyze" />
<data format="png" name="outfile" metadata_source="input" />
**What it does**
This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
**TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
In the following library, most sequences are 24-mers to 27-mers.
This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
.. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png
In the following library, most sequences are 19,22 or 23-mers.
This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
.. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png
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::
If the sequences span over multiple lines::
Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
**Multiplicity counts (a.k.a reads-count)**
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).
Example 1 - The following FASTA file *does not* have multiplicity counts::
Each sequence is counts as one, to produce the following chart:
.. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png
Example 2 - The following FASTA file have multiplicity counts::
The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
.. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png
Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
.. __: http://hannonlab.cshl.edu/fastx_toolkit/
<!-- FASTA-Clipping-Histogram is part of the FASTX-toolkit, by A.Gordon (firstname.lastname@example.org) -->