Mercurial > repos > fastaptamer > fastaptamer_count
comparison fastaptamer_count_1.xml @ 0:2bed8ca187a1 draft
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| author | fastaptamer |
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| date | Tue, 10 Feb 2015 14:22:39 -0500 |
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| -1:000000000000 | 0:2bed8ca187a1 |
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| 1 <tool id="fastaptamer_count_1_0_2" name="FASTAptamer-Count" version="1.0.2"> | |
| 2 | |
| 3 <description>Count, rank, sort and normalize sequence reads in a selection population.</description> | |
| 4 | |
| 5 <version_command>fastaptamer_count -v</version_command> | |
| 6 | |
| 7 <command interpreter="perl">fastaptamer_count -i $input -o $output</command> | |
| 8 | |
| 9 <inputs> | |
| 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> | |
| 11 </inputs> | |
| 12 | |
| 13 <outputs> | |
| 14 <data name="output" format="fasta" label="FASTAptamer-Count output file"></data> | |
| 15 </outputs> | |
| 16 | |
| 17 <help> | |
| 18 | |
| 19 .. class:: warningmark | |
| 20 | |
| 21 FASTAptamer-Count requires FASTQ formatted input files. | |
| 22 | |
| 23 .. class:: infomark | |
| 24 | |
| 25 Input files should be trimmed of constant regions and filtered for only high-quality reads. | |
| 26 | |
| 27 ------ | |
| 28 | |
| 29 **FASTAptamer-Count** serves as the gateway to the FASTAptamer suite of bioinformatics tools for combinatorial selections. | |
| 30 | |
| 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. | |
| 32 | |
| 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: | |
| 34 | |
| 35 >RANK-READS-RPM | |
| 36 | |
| 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. | |
| 38 | |
| 39 ------ | |
| 40 | |
| 41 .. image:: | |
| 42 http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png | |
| 43 :height: 98 | |
| 44 :width: 300 | |
| 45 | |
| 46 For more information on FASTAptamer, visit our website_. | |
| 47 | |
| 48 FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_. | |
| 49 | |
| 50 .. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt | |
| 51 .. _website: http://burkelab.missouri.edu/fastaptamer.html | |
| 52 | |
| 53 </help> | |
| 54 | |
| 55 <citations> | |
| 56 <citation type="doi">doi:10.1038/mtna.2015.4</citation> | |
| 57 </citations> | |
| 58 | |
| 59 </tool> |