Mercurial > repos > devteam > fastx_nucleotides_distribution
annotate fastx_nucleotides_distribution.xml @ 2:05f35740cd79 draft
Uploaded tool help images.
| author | devteam |
|---|---|
| date | Tue, 03 Jun 2014 15:07:52 -0400 |
| parents | f6abd8b6a870 |
| children | 3b6c41fc2d21 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" name="Draw nucleotides distribution chart"> |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
| 5 </requirements> | |
| 6 <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command> | |
| 7 | |
| 8 <inputs> | |
|
1
f6abd8b6a870
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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9 <param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" /> |
| 0 | 10 </inputs> |
| 11 | |
| 12 <outputs> | |
|
1
f6abd8b6a870
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
13 <data format="png" name="output" metadata_source="input" /> |
| 0 | 14 </outputs> |
| 15 <help> | |
| 16 | |
| 17 **What it does** | |
| 18 | |
| 19 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. | |
| 20 | |
| 21 .. class:: infomark | |
| 22 | |
| 23 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. | |
| 24 | |
| 25 ----- | |
| 26 | |
| 27 **Output Examples** | |
| 28 | |
| 29 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** | |
| 30 | |
| 2 | 31 .. image:: fastq_nucleotides_distribution_1.png |
| 0 | 32 |
| 33 In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** | |
| 34 | |
| 2 | 35 .. image:: fastq_nucleotides_distribution_2.png |
| 0 | 36 |
| 37 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): | |
| 38 | |
| 2 | 39 .. image:: fastq_nucleotides_distribution_3.png |
| 0 | 40 |
| 41 But most of the time, the chart will look rather random: | |
| 42 | |
| 2 | 43 .. image:: fastq_nucleotides_distribution_4.png |
| 0 | 44 |
| 45 ------ | |
| 46 | |
| 47 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 48 | |
| 49 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
| 50 | |
| 51 </help> | |
| 52 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | |
| 53 </tool> |