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1 <tool id="generate_coverage_report" name="Polymorphism of the Reads" version="1.0.0">
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2 <description>the percentage of reads supporting each nucleotide at each location</description>
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3 <command interpreter="python">blat_coverage_report.py $input1 $output1</command>
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4 <inputs>
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5 <param name="input1" type="data" format="tabular" label="Alignment result"/>
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6 </inputs>
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7 <outputs>
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8 <data name="output1" format="tabular"/>
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9 </outputs>
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10 <tests>
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11 <test>
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12 <param name="input1" value="blat_coverage_report_test1.txt" ftype="tabular" />
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13 <output name="output1" file="blat_coverage_report_test1.out" />
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14 </test>
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15 </tests>
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16 <help>
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17
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18 .. class:: warningmark
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19
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20 **IMPORTANT**. Only works for BLAT **standard** or **pslx** output formats (hint: to output pslx format, add **-out=pslx** in the command).
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21
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22 -----
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23
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24 **What it does**
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25
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26 The tool will generate a table of 6 columns as following:
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27
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28 - 1st column: chromosome id.
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29
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30 - 2nd column: chromosome location.
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31
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32 - 3rd column: the nucleotide from reference genome at the chromosome location (2nd column).
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33
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34 - 4th column: total coverage of the reads (number of reads that were mapped to the chromosome location).
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35
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36 - 5th column: percentage of reads that support nucleotide **A** at this location.
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37
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38 - 6th column: percentage of reads that support nucleotide **T** at this location.
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39
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40 - 7th column: percentage of reads that support nucleotide **C** at this location.
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41
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42 - 8th column: percentage of reads that support nucleotide **G** at this location.
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43
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44
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45 -----
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46
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47 **Example**
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48
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49 - The BLAT pslx results look like the following (tab separated with sequence at the end)::
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50
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51 30 0 0 0 0 0 0 0 + seq0 30 0 30 chr 4639675 4549207 4549237 1 30, 0, 4549207, cggacagcgccgccaccaacaaagccacca, cggacagcgccgccaccaacaaagccacca,
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52 30 0 0 0 0 0 0 0 + seq1 30 0 30 chr 4639675 614777 614807 1 30, 0, 614777, aaaacaccggatgctccggcgctggcagat, aaaacaccggatgctccggcgctggcagat,
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53 28 1 0 0 0 0 0 0 + seq2 30 0 29 chr 4639675 3289283 3289312 1 29, 0, 3289283, tttgcttttagtacaccggattcagaacc, tttgctttcagtacaccggattcagaacc,
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54 30 0 0 0 0 0 0 0 + seq4 30 0 30 chr 4639675 2665584 2665614 1 30, 0, 2665584, cacgctacgtgcgcccccgcccagaaggcg, cacgctacgtgcgcccccgcccagaaggcg,
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55
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56 The 14th column is the chromosome id, and the 16th and 17th columns shows the reads were mapped to chromosome start and end locations.
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57
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58 - The report showed overall coverage of reads on each chromosome location (partial result)::
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59
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60 +-------+----------+------+------+--------+------+--------+------+
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61 | title | location | ref. | cov. | A | T | C | G |
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62 +-------+----------+------+------+--------+------+--------+------+
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63 | chr | 614777 | A | 1 | A(100) | T(0) | C(0) | G(0) |
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64 | chr | 614778 | A | 1 | A(100) | T(0) | C(0) | G(0) |
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65 | chr | 614779 | A | 1 | A(100) | T(0) | C(0) | G(0) |
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66 +-------+----------+------+------+--------+------+--------+------+
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67
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68 -----
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69
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70 **Reference**
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71
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72 **BLAT**: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664.
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73
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74 </help>
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75 </tool>
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