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annotate test-data/tblastN/readme/README.md @ 3:915aafec8726 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Thu, 14 Jul 2016 13:15:05 -0400
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1 Conversion of NCBI BLAST+ tblastn results to PSL format
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2 =======================================================
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3 Wilson Leung <wleung@wustl.edu>
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5 Last Update: 04/24/2016
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8 Version information
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9 -------------------
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10 * Kent source tree: v324
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11 * NCBI BLAST+: BLAST 2.2.30+
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13 Data sources
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14 -------------------
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15 For testing purposes, the database consists of only contig1 in the Dbia3 assembly while the protein sequences correspond to the three isoforms of the *D. melanogaster* *ci* gene in contig1. The protein sequences are available through [FlyBase](http://flybase.org/cgi-bin/getseq.html?source=dmel&id=FBgn0004859&chr=4&dump=PrecompiledFasta&targetset=translation).
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17 * Dbia3.fa = contig1 sequence in the Dbia3 asssembly
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18 * ci.pep = Protein sequences for the three isoforms of the *ci* gene in *D. melanogaster*
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20 Conversion protocol
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21 -----------------------
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22 1. Create BLAST database for the assembly
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23 ```
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24 makeblastdb -in Dbia3.fa -dbtype nucl
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25 ```
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27 2. Perform tblastn search and output results in XML format
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28 ```
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29 tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2
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30 ```
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32 3. Convert results into PSL format
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33 ```
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34 blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl
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35 ```
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37 4. Convert PSL output into BED format
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38 ```
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39 pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed
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40 ```
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42 Output files
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43 -----------------------
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44 * tblastn_Dbia3_ci.xml = tblastn results in XML format
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45 * tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format
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46 * tblastn_Dbia3_ci.xml.bed = tblastn results in BED format
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