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1 <tool id="fastaptamer_count_1_0_1" name="FASTAptamer-Count" version="1.0.1">
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2
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3 <description>Count, rank, sort and normalize sequence reads in a selection population.</description>
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4
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5 <version_command>fastaptamer_count -v</version_command>
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6
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7 <command interpreter="perl">fastaptamer_count -i $input -o $output</command>
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8
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9 <inputs>
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10 <param name="input" type="data" format="fastq" label="Input file" help="Must be FASTQ and should be pre-processed (filtered for quality and trimmed of constant regions)."></param>
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11 </inputs>
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12
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13 <outputs>
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14 <data name="output" format="fasta" label="FASTAptamer-Count output file"></data>
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15 </outputs>
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16
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17 <help>
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18
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19 .. class:: warningmark
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20
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21 FASTAptamer-Count requires FASTQ formatted input files.
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22
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23 .. class:: infomark
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24
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25 Input files should be trimmed of constant regions and filtered for only high-quality reads.
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26
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27 ------
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28
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29 **FASTAptamer-Count** serves as the gateway to the FASTAptamer suite of bioinformatics tools for combinatorial selections.
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30
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31 For a given FASTQ input file, FASTAptamer-Count will determine the number of times each sequence was read, normalize sequence frequency to reads per million, and rank and sort sequences by decreasing total reads.
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32
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33 Output is generated as a sorted and non-redundant FASTA formatted file in which each unique sequence generates a FASTA entry with the following information in the description line:
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34
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35 >RANK-READS-RPM
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36
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37 RANK is the relative abundance of the sequence within the population. In cases where two or more sequences are sampled with equal abundance, FASTAptamer-Count follows standard competition ranking (e.g., “1-2-2-4” where two sequences are tied for second). READS is the raw number of times a sequence was counted. RPM is “Reads per million,” which is a normalized value that allows for comparison across populations of varying read depth. RPM is calculated as: RPM = (READS/(population size)) x 10^6.
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38
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39 ------
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40
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41 .. image::
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42 http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png
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43 :height: 98
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44 :width: 300
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45
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46 For more information on FASTAptamer, visit our website_.
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47
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48 FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_.
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49
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50 .. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt
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51 .. _website: http://burkelab.missouri.edu/fastaptamer.html
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52
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53 </help>
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54
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55 <citations>
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56 <citation type="doi">doi:10.1038/mtna.2015.7x</citation>
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57 </citations>
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58
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59 </tool>
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